Jan-06 22:25:17.989 [main] DEBUG nextflow.cli.Launcher - $> nextflow -trace nextflow.k8s run systemsgenetics/kinc-nf -name goofy-bartik Jan-06 22:25:19.027 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 19.07.0 Jan-06 22:25:21.161 [main] DEBUG nextflow.scm.AssetManager - Git config: /workspace/projects/systemsgenetics/kinc-nf/.git/config; branch: master; remote: origin; url: https://github.com/SystemsGenetics/KINC-nf.git Jan-06 22:25:21.172 [main] DEBUG nextflow.scm.AssetManager - Git config: /workspace/projects/systemsgenetics/kinc-nf/.git/config; branch: master; remote: origin; url: https://github.com/SystemsGenetics/KINC-nf.git Jan-06 22:25:22.412 [main] DEBUG nextflow.scm.AssetManager - Git config: /workspace/projects/systemsgenetics/kinc-nf/.git/config; branch: master; remote: origin; url: https://github.com/SystemsGenetics/KINC-nf.git Jan-06 22:25:22.413 [main] INFO nextflow.cli.CmdRun - Launching `systemsgenetics/kinc-nf` [goofy-bartik] - revision: 2514283b07 [master] Jan-06 22:25:23.712 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /workspace/projects/systemsgenetics/kinc-nf/nextflow.config Jan-06 22:25:23.781 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /workspace/cole/nextflow.config Jan-06 22:25:23.782 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /workspace/projects/systemsgenetics/kinc-nf/nextflow.config Jan-06 22:25:23.782 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /workspace/cole/nextflow.config Jan-06 22:25:23.791 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` Jan-06 22:25:23.989 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` Jan-06 22:25:24.156 [main] DEBUG nextflow.Session - Session uuid: c54aeda8-b621-435b-bff2-78db026e8ab0 Jan-06 22:25:24.157 [main] DEBUG nextflow.Session - Run name: goofy-bartik Jan-06 22:25:24.157 [main] DEBUG nextflow.Session - Executor pool size: 2 Jan-06 22:25:24.171 [main] DEBUG nextflow.cli.CmdRun - Version: 19.07.0 build 5106 Created: 27-07-2019 13:22 UTC (13:22 GMT) System: Linux 5.3.2-1.el7.x86_64 Runtime: Groovy 2.5.6 on OpenJDK 64-Bit Server VM 1.8.0_212-b04 Encoding: UTF-8 (UTF-8) Process: 8@goofy-bartik [10.244.218.137] CPUs: 1 - Mem: 31.4 GB (17.4 GB) - Swap: 0 (0) Jan-06 22:25:25.688 [main] DEBUG nextflow.Session - Work-dir: /workspace/cole/work [ceph] Jan-06 22:25:25.688 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /workspace/projects/systemsgenetics/kinc-nf/bin Jan-06 22:25:28.892 [main] DEBUG nextflow.Session - Session start invoked Jan-06 22:25:28.899 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /workspace/cole/output/reports/trace.txt Jan-06 22:25:31.833 [main] WARN nextflow.script.ScriptRunner - Nextflow version 19.07.0 does not match workflow required version: >=19.10.0 -- Execution will continue, but things may break! Jan-06 22:25:31.834 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jan-06 22:25:31.895 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: input/; pattern: *.emx.txt; options: [:] Jan-06 22:25:32.010 [PathVisitor-2] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: input/; pattern: *.emx; options: [:] Jan-06 22:25:32.017 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: input/; pattern: *.cmx.txt; options: [:] Jan-06 22:25:32.023 [PathVisitor-4] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: input/; pattern: *.ccm; options: [:] Jan-06 22:25:32.025 [PathVisitor-5] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: input/; pattern: *.cmx; options: [:] Jan-06 22:25:32.027 [PathVisitor-6] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: input/; pattern: *.rmt.txt; options: [:] Jan-06 22:25:32.029 [PathVisitor-7] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: input/; pattern: *.coexpnet.txt; options: [:] Jan-06 22:25:32.150 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: k8s Jan-06 22:25:32.150 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'k8s' Jan-06 22:25:32.157 [main] DEBUG nextflow.executor.Executor - [warm up] executor > k8s Jan-06 22:25:32.162 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'k8s' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Jan-06 22:25:32.224 [main] DEBUG nextflow.k8s.client.ConfigDiscovery - K8s config file does not exist: /root/.kube/config Jan-06 22:25:32.238 [main] DEBUG nextflow.k8s.K8sExecutor - [K8s] API client config=ClientConfig[ server=10.96.0.1:443, namespace=deepgtex-prp, token=eyJhbGciOiJ.., sslCert=LS0tLS1CRUd.., clientCert=-, clientKey=-, verifySsl=false, fromFile=true ] Jan-06 22:25:32.276 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > import_emx -- maxForks: 2 Jan-06 22:25:32.339 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: k8s Jan-06 22:25:32.339 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'k8s' Jan-06 22:25:32.341 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > export_emx -- maxForks: 2 Jan-06 22:25:32.359 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:gpu` matches label `gpu` for process with name similarity_chunk Jan-06 22:25:32.360 [main] WARN nextflow.script.ProcessConfig - Unknown directive `accelerator` for process `similarity_chunk` Jan-06 22:25:32.360 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:similarity_chunk` matches process similarity_chunk Jan-06 22:25:32.361 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: k8s Jan-06 22:25:32.361 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'k8s' Jan-06 22:25:32.405 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [1] Jan-06 22:25:32.412 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > similarity_chunk -- maxForks: 2 Jan-06 22:25:32.422 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: k8s Jan-06 22:25:32.422 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'k8s' Jan-06 22:25:32.423 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > similarity_merge -- maxForks: 2 Jan-06 22:25:32.434 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:gpu` matches label `gpu` for process with name similarity_mpi Jan-06 22:25:32.434 [main] WARN nextflow.script.ProcessConfig - Unknown directive `accelerator` for process `similarity_mpi` Jan-06 22:25:32.435 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:similarity_mpi` matches process similarity_mpi Jan-06 22:25:32.435 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: k8s Jan-06 22:25:32.435 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'k8s' Jan-06 22:25:32.438 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > similarity_mpi -- maxForks: 2 Jan-06 22:25:32.470 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: k8s Jan-06 22:25:32.470 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'k8s' Jan-06 22:25:32.472 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > import_cmx -- maxForks: 2 Jan-06 22:25:32.485 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: k8s Jan-06 22:25:32.485 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'k8s' Jan-06 22:25:32.486 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > export_cmx -- maxForks: 2 Jan-06 22:25:32.490 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:threshold` matches process threshold Jan-06 22:25:32.490 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: k8s Jan-06 22:25:32.490 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'k8s' Jan-06 22:25:32.491 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > threshold -- maxForks: 2 Jan-06 22:25:32.498 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: k8s Jan-06 22:25:32.498 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'k8s' Jan-06 22:25:32.499 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > extract -- maxForks: 2 Jan-06 22:25:32.505 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: k8s Jan-06 22:25:32.505 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'k8s' Jan-06 22:25:32.506 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > visualize -- maxForks: 2 Jan-06 22:25:32.507 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Jan-06 22:25:32.507 [main] DEBUG nextflow.Session - Session await Jan-06 22:25:32.692 [Actor Thread 9] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > import_emx (Yeast) -- work folder: /workspace/cole/work/78/f779d33faa273a5b0061ef1098c577 Jan-06 22:25:33.171 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-78f779d33faa273a5b0061ef1098c577", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "import_emx_Yeast", "processName": "import_emx", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-78f779d33faa273a5b0061ef1098c577", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/f779d33faa273a5b0061ef1098c577", "volumeMounts": [ { "name": "vol-1", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-1", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:25:33.468 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-78f779d33faa273a5b0061ef1098c577", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-78f779d33faa273a5b0061ef1098c577", "uid": "628f23ca-c6ab-4a48-be49-dd6727048996", "resourceVersion": "1070847202", "creationTimestamp": "2020-01-06T22:25:33Z", "labels": { "app": "nextflow", "processName": "import_emx", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "import_emx_Yeast" }, "annotations": { "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-78f779d33faa273a5b0061ef1098c577; memory limit for container nf-78f779d33faa273a5b0061ef1098c577", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-1", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-78f779d33faa273a5b0061ef1098c577", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/f779d33faa273a5b0061ef1098c577", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-1", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Burstable" } } Jan-06 22:25:33.478 [Task submitter] INFO nextflow.Session - [78/f779d3] Submitted process > import_emx (Yeast) Jan-06 22:25:37.190 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-78f779d33faa273a5b0061ef1098c577/status Jan-06 22:25:37.464 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-78f779d33faa273a5b0061ef1098c577/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-78f779d33faa273a5b0061ef1098c577", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-78f779d33faa273a5b0061ef1098c577/status", "uid": "628f23ca-c6ab-4a48-be49-dd6727048996", "resourceVersion": "1070847289", "creationTimestamp": "2020-01-06T22:25:33Z", "labels": { "app": "nextflow", "processName": "import_emx", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "import_emx_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.12/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-78f779d33faa273a5b0061ef1098c577; memory limit for container nf-78f779d33faa273a5b0061ef1098c577", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-1", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-78f779d33faa273a5b0061ef1098c577", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/f779d33faa273a5b0061ef1098c577", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-1", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:33Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:33Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-78f779d33faa273a5b0061ef1098c577]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:33Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-78f779d33faa273a5b0061ef1098c577]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:33Z" } ], "hostIP": "130.191.103.1", "startTime": "2020-01-06T22:25:33Z", "containerStatuses": [ { "name": "nf-78f779d33faa273a5b0061ef1098c577", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Burstable" } } Jan-06 22:25:42.190 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-78f779d33faa273a5b0061ef1098c577/status Jan-06 22:25:42.461 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-78f779d33faa273a5b0061ef1098c577/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-78f779d33faa273a5b0061ef1098c577", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-78f779d33faa273a5b0061ef1098c577/status", "uid": "628f23ca-c6ab-4a48-be49-dd6727048996", "resourceVersion": "1070847462", "creationTimestamp": "2020-01-06T22:25:33Z", "labels": { "app": "nextflow", "processName": "import_emx", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "import_emx_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.12/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-78f779d33faa273a5b0061ef1098c577; memory limit for container nf-78f779d33faa273a5b0061ef1098c577", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-1", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-78f779d33faa273a5b0061ef1098c577", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/f779d33faa273a5b0061ef1098c577", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-1", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:33Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:37Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:37Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:33Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.12", "podIPs": [ { "ip": "10.244.14.12" } ], "startTime": "2020-01-06T22:25:33Z", "containerStatuses": [ { "name": "nf-78f779d33faa273a5b0061ef1098c577", "state": { "running": { "startedAt": "2020-01-06T22:25:36Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://cd26b9705af80d781708055dceb5f48033913944d46e3b75155359144e7a0caf", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:25:47.189 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-78f779d33faa273a5b0061ef1098c577/status Jan-06 22:25:47.457 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-78f779d33faa273a5b0061ef1098c577/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-78f779d33faa273a5b0061ef1098c577", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-78f779d33faa273a5b0061ef1098c577/status", "uid": "628f23ca-c6ab-4a48-be49-dd6727048996", "resourceVersion": "1070847922", "creationTimestamp": "2020-01-06T22:25:33Z", "labels": { "app": "nextflow", "processName": "import_emx", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "import_emx_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.12/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-78f779d33faa273a5b0061ef1098c577; memory limit for container nf-78f779d33faa273a5b0061ef1098c577", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-1", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-78f779d33faa273a5b0061ef1098c577", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/f779d33faa273a5b0061ef1098c577", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-1", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:33Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:44Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:44Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:33Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.12", "podIPs": [ { "ip": "10.244.14.12" } ], "startTime": "2020-01-06T22:25:33Z", "containerStatuses": [ { "name": "nf-78f779d33faa273a5b0061ef1098c577", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:36Z", "finishedAt": "2020-01-06T22:25:43Z", "containerID": "docker://cd26b9705af80d781708055dceb5f48033913944d46e3b75155359144e7a0caf" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://cd26b9705af80d781708055dceb5f48033913944d46e3b75155359144e7a0caf", "started": false } ], "qosClass": "Burstable" } } Jan-06 22:25:47.896 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-78f779d33faa273a5b0061ef1098c577 Jan-06 22:25:48.185 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-78f779d33faa273a5b0061ef1098c577 { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-78f779d33faa273a5b0061ef1098c577", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-78f779d33faa273a5b0061ef1098c577", "uid": "628f23ca-c6ab-4a48-be49-dd6727048996", "resourceVersion": "1070848157", "creationTimestamp": "2020-01-06T22:25:33Z", "deletionTimestamp": "2020-01-06T22:25:48Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "import_emx", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "import_emx_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.12/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-78f779d33faa273a5b0061ef1098c577; memory limit for container nf-78f779d33faa273a5b0061ef1098c577", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-1", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-78f779d33faa273a5b0061ef1098c577", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/f779d33faa273a5b0061ef1098c577", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-1", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:33Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:44Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:44Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:33Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.12", "podIPs": [ { "ip": "10.244.14.12" } ], "startTime": "2020-01-06T22:25:33Z", "containerStatuses": [ { "name": "nf-78f779d33faa273a5b0061ef1098c577", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:36Z", "finishedAt": "2020-01-06T22:25:43Z", "containerID": "docker://cd26b9705af80d781708055dceb5f48033913944d46e3b75155359144e7a0caf" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://cd26b9705af80d781708055dceb5f48033913944d46e3b75155359144e7a0caf", "started": false } ], "qosClass": "Burstable" } } Jan-06 22:25:48.186 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: import_emx (Yeast); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/78/f779d33faa273a5b0061ef1098c577] Jan-06 22:25:48.528 [Actor Thread 15] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > similarity_chunk (Yeast/1) -- work folder: /workspace/cole/work/78/93a740ff351bb12ef0e827764db951 Jan-06 22:25:48.664 [Actor Thread 7] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > similarity_chunk (Yeast/0) -- work folder: /workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac Jan-06 22:25:48.743 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "similarity_chunk_Yeast_1", "processName": "similarity_chunk", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "resources": { "limits": { "cpu": 1, "memory": "8192Mi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:25:48.928 [Actor Thread 7] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > similarity_chunk (Yeast/3) -- work folder: /workspace/cole/work/fc/893f9b03580034e37b00f5f574e016 Jan-06 22:25:48.944 [Actor Thread 15] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > similarity_chunk (Yeast/2) -- work folder: /workspace/cole/work/77/9c86765929b9fb8181031d38b6aace Jan-06 22:25:49.041 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848222", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Guaranteed" } } Jan-06 22:25:49.042 [Task submitter] INFO nextflow.Session - [78/93a740] Submitted process > similarity_chunk (Yeast/1) Jan-06 22:25:49.159 [Actor Thread 15] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > similarity_chunk (Yeast/5) -- work folder: /workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5 Jan-06 22:25:49.204 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "similarity_chunk_Yeast_0", "processName": "similarity_chunk", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "resources": { "limits": { "cpu": 1, "memory": "8192Mi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:25:49.207 [Actor Thread 7] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > similarity_chunk (Yeast/4) -- work folder: /workspace/cole/work/cb/31425e6430d196fa7514811c699f20 Jan-06 22:25:49.693 [Actor Thread 7] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > similarity_chunk (Yeast/7) -- work folder: /workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65 Jan-06 22:25:49.693 [Actor Thread 15] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > similarity_chunk (Yeast/6) -- work folder: /workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de Jan-06 22:25:49.770 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848274", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Guaranteed" } } Jan-06 22:25:49.771 [Task submitter] INFO nextflow.Session - [e4/125907] Submitted process > similarity_chunk (Yeast/0) Jan-06 22:25:49.903 [Actor Thread 7] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > similarity_chunk (Yeast/9) -- work folder: /workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a Jan-06 22:25:49.916 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "similarity_chunk_Yeast_3", "processName": "similarity_chunk", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "resources": { "limits": { "cpu": 1, "memory": "8192Mi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:25:50.024 [Actor Thread 15] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > similarity_chunk (Yeast/8) -- work folder: /workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75 Jan-06 22:25:50.215 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848305", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Guaranteed" } } Jan-06 22:25:50.215 [Task submitter] INFO nextflow.Session - [fc/893f9b] Submitted process > similarity_chunk (Yeast/3) Jan-06 22:25:50.360 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "similarity_chunk_Yeast_2", "processName": "similarity_chunk", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "resources": { "limits": { "cpu": 1, "memory": "8192Mi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:25:50.639 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070848338", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Guaranteed" } } Jan-06 22:25:50.640 [Task submitter] INFO nextflow.Session - [77/9c8676] Submitted process > similarity_chunk (Yeast/2) Jan-06 22:25:50.853 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "similarity_chunk_Yeast_5", "processName": "similarity_chunk", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "resources": { "limits": { "cpu": 1, "memory": "8192Mi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:25:51.133 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848380", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Guaranteed" } } Jan-06 22:25:51.134 [Task submitter] INFO nextflow.Session - [89/36f536] Submitted process > similarity_chunk (Yeast/5) Jan-06 22:25:51.346 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "similarity_chunk_Yeast_4", "processName": "similarity_chunk", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "resources": { "limits": { "cpu": 1, "memory": "8192Mi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:25:51.622 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848428", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Guaranteed" } } Jan-06 22:25:51.623 [Task submitter] INFO nextflow.Session - [cb/31425e] Submitted process > similarity_chunk (Yeast/4) Jan-06 22:25:51.822 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "similarity_chunk_Yeast_7", "processName": "similarity_chunk", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "resources": { "limits": { "cpu": 1, "memory": "8192Mi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:25:52.102 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848480", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Guaranteed" } } Jan-06 22:25:52.102 [Task submitter] INFO nextflow.Session - [d3/7d730f] Submitted process > similarity_chunk (Yeast/7) Jan-06 22:25:52.190 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:25:52.251 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "similarity_chunk_Yeast_6", "processName": "similarity_chunk", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "resources": { "limits": { "cpu": 1, "memory": "8192Mi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:25:52.464 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848419", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-7893a740ff351bb12ef0e827764db951]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-7893a740ff351bb12ef0e827764db951]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:25:52.548 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848529", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Guaranteed" } } Jan-06 22:25:52.710 [Task submitter] INFO nextflow.Session - [cf/b9ed98] Submitted process > similarity_chunk (Yeast/6) Jan-06 22:25:52.710 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:25:52.854 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "similarity_chunk_Yeast_9", "processName": "similarity_chunk", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "resources": { "limits": { "cpu": 1, "memory": "8192Mi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:25:52.976 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:25:52.979 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:25:53.132 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848594", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Guaranteed" } } Jan-06 22:25:53.132 [Task submitter] INFO nextflow.Session - [50/96a67a] Submitted process > similarity_chunk (Yeast/9) Jan-06 22:25:53.264 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848398", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-fc893f9b03580034e37b00f5f574e016]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-fc893f9b03580034e37b00f5f574e016]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:25:53.265 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:25:53.276 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "similarity_chunk_Yeast_8", "processName": "similarity_chunk", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "resources": { "limits": { "cpu": 1, "memory": "8192Mi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:25:53.562 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070848534", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-779c86765929b9fb8181031d38b6aace]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-779c86765929b9fb8181031d38b6aace]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:25:53.563 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:25:53.590 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070848623", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Guaranteed" } } Jan-06 22:25:53.591 [Task submitter] INFO nextflow.Session - [28/d955cf] Submitted process > similarity_chunk (Yeast/8) Jan-06 22:25:53.871 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848610", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-8936f53648905107a56f3ff27d4c8fd5]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-8936f53648905107a56f3ff27d4c8fd5]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:25:53.872 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:25:54.139 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848586", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-cb31425e6430d196fa7514811c699f20]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-cb31425e6430d196fa7514811c699f20]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:25:54.140 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:25:54.420 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848674", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-d37d730fe8dfbd3d1e26e0d26c301f65]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-d37d730fe8dfbd3d1e26e0d26c301f65]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:25:57.191 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:25:57.462 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:25:57.464 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:25:57.735 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:25:57.737 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:25:58.003 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:25:58.005 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:25:58.272 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070848892", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-779c86765929b9fb8181031d38b6aace]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-779c86765929b9fb8181031d38b6aace]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:25:58.273 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:25:58.596 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:25:58.599 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:25:58.884 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:25:58.887 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:25:59.153 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:25:59.155 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:25:59.422 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:25:59.424 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:25:59.701 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:25:59.703 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:25:59.972 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070848797", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-28d955cf18e9764e53c797fe53b2bf75]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-28d955cf18e9764e53c797fe53b2bf75]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:26:02.190 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:26:02.458 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:02.460 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:26:02.732 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:02.735 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:26:03.010 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:03.012 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:26:03.277 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:03.279 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:26:03.567 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:03.569 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:26:03.834 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:03.836 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:26:04.102 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:04.105 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:26:04.380 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:04.383 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:26:04.654 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:04.656 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:26:04.936 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070848797", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-28d955cf18e9764e53c797fe53b2bf75]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-28d955cf18e9764e53c797fe53b2bf75]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:26:07.190 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:26:07.456 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:07.459 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:26:07.725 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:07.728 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:26:08.000 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:08.003 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:26:08.279 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:08.282 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:26:08.554 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:08.556 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:26:08.838 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:08.840 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:26:09.109 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:09.111 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:26:09.377 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:09.379 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:26:09.644 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:09.647 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:26:09.912 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:12.190 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:26:12.458 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:12.461 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:26:12.726 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:12.729 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:26:12.997 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:12.999 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:26:13.271 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:13.273 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:26:13.537 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:13.540 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:26:13.804 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:13.806 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:26:14.102 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:14.104 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:26:14.373 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:14.375 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:26:14.639 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:14.641 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:26:14.910 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:17.190 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:26:17.527 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:17.529 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:26:17.813 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:17.815 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:26:18.086 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:18.088 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:26:18.355 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:18.357 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:26:18.624 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:18.627 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:26:18.891 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:18.893 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:26:19.161 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:19.164 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:26:19.440 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:19.443 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:26:19.715 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:19.717 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:26:19.987 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:22.191 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:26:22.455 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:22.458 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:26:22.723 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:22.725 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:26:22.989 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:22.991 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:26:23.256 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:23.326 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:26:23.592 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:23.594 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:26:23.859 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:23.861 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:26:24.135 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:24.137 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:26:24.402 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:24.404 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:26:24.675 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:24.677 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:26:24.942 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:27.191 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:26:27.456 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:27.458 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:26:27.736 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:27.738 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:26:28.004 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:28.006 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:26:28.271 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:28.273 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:26:28.539 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:28.541 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:26:28.806 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:28.808 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:26:29.074 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:29.076 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:26:29.342 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:29.344 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:26:29.613 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:29.615 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:26:29.883 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:32.192 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:26:32.457 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:32.459 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:26:32.740 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:32.742 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:26:33.016 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:33.018 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:26:33.289 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:33.291 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:26:33.556 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:33.558 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:26:33.831 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:33.833 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:26:34.097 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:34.099 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:26:34.377 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:34.379 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:26:34.657 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:34.660 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:26:34.925 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:37.192 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:26:37.468 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:37.470 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:26:37.768 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:37.771 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:26:38.036 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:38.038 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:26:38.314 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:38.316 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:26:38.586 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:38.588 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:26:38.857 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:38.859 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:26:39.126 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:39.128 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:26:39.403 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:39.405 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:26:39.670 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:39.672 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:26:39.943 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:42.193 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:26:42.463 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:42.466 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:26:42.733 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:42.734 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:26:43.006 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:43.008 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:26:43.272 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:43.274 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:26:43.538 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:43.540 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:26:43.804 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:43.806 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:26:44.069 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:44.071 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:26:44.335 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:44.336 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:26:44.606 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:44.607 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:26:44.872 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:47.194 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:26:47.458 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:47.460 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:26:47.725 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:47.727 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:26:47.996 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:47.997 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:26:48.263 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:48.265 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:26:48.542 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:48.544 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:26:48.821 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:48.823 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:26:49.091 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:49.093 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:26:49.358 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:49.359 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:26:49.631 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:49.632 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:26:49.896 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:52.194 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:26:52.458 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:52.460 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:26:52.732 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:52.734 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:26:53.003 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:53.005 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:26:53.269 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:53.271 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:26:53.535 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:53.537 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:26:53.801 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:54.050 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:26:54.314 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:54.315 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:26:54.580 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:54.582 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:26:54.846 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:54.848 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:26:55.112 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:57.193 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:26:57.464 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:57.466 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:26:57.730 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:57.732 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:26:57.995 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:57.997 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:26:58.267 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:58.270 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:26:58.542 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:58.544 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:26:58.815 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:58.817 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:26:59.081 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:59.082 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:26:59.368 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:59.370 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:26:59.634 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:26:59.637 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:26:59.908 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:02.193 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:27:02.461 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:02.463 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:27:02.726 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:02.728 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:27:03.015 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:03.016 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:27:03.280 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:03.282 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:27:03.546 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:03.548 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:27:03.812 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:03.813 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:27:04.076 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:04.078 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:27:04.342 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:04.343 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:27:04.607 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:04.609 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:27:04.872 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:07.193 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:27:07.458 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:07.460 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:27:07.729 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:07.730 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:27:07.998 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:08.000 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:27:08.267 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:08.268 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:27:08.533 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:08.535 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:27:08.821 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:08.823 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:27:09.086 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:09.088 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:27:09.357 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:09.358 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:27:09.622 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:09.624 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:27:09.899 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:12.193 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:27:12.466 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:12.467 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:27:12.735 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:12.736 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:27:12.999 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:13.001 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:27:13.276 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:13.278 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:27:13.543 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:13.545 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:27:13.810 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:13.811 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:27:14.075 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:14.077 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:27:14.349 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:14.351 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:27:14.616 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:14.617 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:27:14.884 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:17.193 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:27:17.473 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070848588", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:17.543 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:27:17.806 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:17.808 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:27:18.072 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:18.074 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:27:18.338 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:18.340 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:27:18.610 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:18.612 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:27:18.881 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:18.883 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:27:19.159 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:19.161 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:27:19.426 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:19.428 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:27:19.693 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:19.694 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:27:19.963 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:22.194 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status Jan-06 22:27:22.463 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951/status", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070853634", "creationTimestamp": "2020-01-06T22:25:48Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:27:21Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:27:21Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:51Z", "finishedAt": "2020-01-06T22:27:21Z", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:27:23.651 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951 Jan-06 22:27:23.932 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951 { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-7893a740ff351bb12ef0e827764db951", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-7893a740ff351bb12ef0e827764db951", "uid": "61ba4e43-1321-490e-924d-39d96e69ce1e", "resourceVersion": "1070853784", "creationTimestamp": "2020-01-06T22:25:48Z", "deletionTimestamp": "2020-01-06T22:27:23Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_1" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.208/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-2", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/78/93a740ff351bb12ef0e827764db951", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-2", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:27:21Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:27:21Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.208", "podIPs": [ { "ip": "10.244.180.208" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-7893a740ff351bb12ef0e827764db951", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:51Z", "finishedAt": "2020-01-06T22:27:21Z", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://2198e411b54fbd0b14cb28092b50a456a4bc88301522e2582dbb2b9fab413414", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:27:23.932 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: similarity_chunk (Yeast/1); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/78/93a740ff351bb12ef0e827764db951] Jan-06 22:27:26.280 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:27:26.569 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:26.571 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:27:26.840 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:26.842 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:27:27.108 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:27.110 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:27:27.374 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:27.375 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:27:27.651 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:27.652 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:27:27.932 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:27.934 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:27:28.202 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:28.203 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:27:28.470 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:28.472 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:27:28.748 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:28.749 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:27:29.026 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:29.028 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:27:29.316 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070848606", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:29.317 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:27:29.584 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:29.586 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:27:29.855 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:29.857 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:27:30.121 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:30.123 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:27:30.387 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:30.388 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:27:30.660 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:30.662 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:27:30.926 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:30.928 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:27:31.198 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:33.750 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:27:34.014 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:34.015 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status Jan-06 22:27:34.286 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016/status", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070854279", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:27:33Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:27:33Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:51Z", "finishedAt": "2020-01-06T22:27:33Z", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:27:35.344 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016 Jan-06 22:27:35.642 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016 { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-fc893f9b03580034e37b00f5f574e016", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-fc893f9b03580034e37b00f5f574e016", "uid": "fa6ce919-bd70-4225-a558-c858b2929052", "resourceVersion": "1070854370", "creationTimestamp": "2020-01-06T22:25:50Z", "deletionTimestamp": "2020-01-06T22:27:35Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_3" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.150.90/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-4", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/fc/893f9b03580034e37b00f5f574e016", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-4", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-5.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:27:33Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:27:33Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "169.228.132.17", "podIP": "10.244.150.90", "podIPs": [ { "ip": "10.244.150.90" } ], "startTime": "2020-01-06T22:25:50Z", "containerStatuses": [ { "name": "nf-fc893f9b03580034e37b00f5f574e016", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:51Z", "finishedAt": "2020-01-06T22:27:33Z", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://1d3441e413d22146d6b832e335d9b192153a171ec6b88e3e7dab16163ec7c72f", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:27:35.642 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: similarity_chunk (Yeast/3); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/fc/893f9b03580034e37b00f5f574e016] Jan-06 22:27:39.198 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:27:39.483 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:39.484 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:27:39.748 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:39.749 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:27:40.016 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:40.018 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:27:40.282 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:40.283 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:27:40.547 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:40.549 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:27:40.813 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:40.814 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:27:41.085 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:41.087 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:27:41.352 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:41.353 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:27:41.617 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:41.618 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:27:41.889 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:41.891 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:27:42.162 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:42.164 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:27:42.439 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:42.441 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:27:42.709 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:42.717 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:27:42.988 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:42.990 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:27:43.265 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:46.087 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:27:46.356 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:46.357 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:27:46.622 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:46.624 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:27:46.900 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:46.902 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:27:47.176 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070848743", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "running": { "startedAt": "2020-01-06T22:25:53Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:47.178 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:27:47.453 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:47.455 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:27:47.725 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:47.727 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:27:48.017 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:48.019 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:27:48.285 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:51.087 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:27:51.352 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:51.353 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:27:51.629 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:51.630 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:27:51.894 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:51.896 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status Jan-06 22:27:52.170 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20/status", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070855247", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:27:51Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:27:51Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:53Z", "finishedAt": "2020-01-06T22:27:50Z", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:27:52.789 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20 Jan-06 22:27:53.062 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20 { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cb31425e6430d196fa7514811c699f20", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cb31425e6430d196fa7514811c699f20", "uid": "2144b075-362f-4acf-9d5c-91ca95db96fc", "resourceVersion": "1070855323", "creationTimestamp": "2020-01-06T22:25:51Z", "deletionTimestamp": "2020-01-06T22:27:53Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_4" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.159.248/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-7", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cb/31425e6430d196fa7514811c699f20", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-7", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-haosu-04.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:27:51Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:27:51Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.51.229", "podIP": "10.244.159.248", "podIPs": [ { "ip": "10.244.159.248" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-cb31425e6430d196fa7514811c699f20", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:53Z", "finishedAt": "2020-01-06T22:27:50Z", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://cb0a903573268081f8ba0971ad0e8a8173bb75fcdf0ac548bb233d438976b49f", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:27:53.062 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: similarity_chunk (Yeast/4); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/cb/31425e6430d196fa7514811c699f20] Jan-06 22:27:57.834 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:27:58.190 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:58.420 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:27:58.692 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:58.762 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:27:59.026 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:59.028 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:27:59.292 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:27:59.649 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:28:00.210 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:00.595 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:28:01.234 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:01.529 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:28:02.177 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:02.582 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:28:03.241 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:03.640 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:28:04.441 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:04.832 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:28:05.601 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:05.972 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:28:06.635 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:07.040 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:28:07.694 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:08.184 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:28:08.863 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:09.244 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:28:09.918 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:10.291 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:28:10.980 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:11.389 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:28:12.066 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:12.757 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:28:13.522 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:14.097 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:28:14.805 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:15.476 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:28:16.237 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:16.667 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:28:17.614 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070849146", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:59Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "running": { "startedAt": "2020-01-06T22:25:58Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:18.132 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:28:18.849 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:19.291 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:28:20.021 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:20.644 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:28:21.346 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:21.793 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:28:22.779 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070848799", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:23.136 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:28:23.762 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:24.205 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:28:24.892 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:25.320 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:28:25.977 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:26.337 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:28:26.973 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070848931", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:56Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "running": { "startedAt": "2020-01-06T22:25:55Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:27.345 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:28:28.099 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:28.470 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:28:29.102 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:29.514 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:28:30.148 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070848443", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "running": { "startedAt": "2020-01-06T22:25:51Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:30.512 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:28:31.150 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070856884", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:27Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:27Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:58Z", "finishedAt": "2020-01-06T22:28:27Z", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:28:31.524 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status Jan-06 22:28:32.173 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace/status", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070856884", "creationTimestamp": "2020-01-06T22:25:50Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:27Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:27Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:58Z", "finishedAt": "2020-01-06T22:28:27Z", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:28:33.428 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace Jan-06 22:28:34.130 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-779c86765929b9fb8181031d38b6aace", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-779c86765929b9fb8181031d38b6aace", "uid": "e3aa5a07-443e-4c38-a0f5-779f4be49ee2", "resourceVersion": "1070857147", "creationTimestamp": "2020-01-06T22:25:50Z", "deletionTimestamp": "2020-01-06T22:28:34Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_2" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.102.16/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-5", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/77/9c86765929b9fb8181031d38b6aace", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-5", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-bharadia-01.sdsc.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:27Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:27Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:50Z" } ], "hostIP": "67.58.50.234", "podIP": "10.244.102.16", "podIPs": [ { "ip": "10.244.102.16" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-779c86765929b9fb8181031d38b6aace", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:58Z", "finishedAt": "2020-01-06T22:28:27Z", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://7f26eaf43383cc77fccdc4c0e0a7a11804e3822e0d96b33e29930d9249229043", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:28:34.546 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: similarity_chunk (Yeast/2); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/77/9c86765929b9fb8181031d38b6aace] Jan-06 22:28:35.385 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:28:36.050 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:36.458 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:28:37.122 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:37.517 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:28:38.357 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070856968", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:29Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:29Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:55Z", "finishedAt": "2020-01-06T22:28:28Z", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:28:38.748 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status Jan-06 22:28:39.446 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65/status", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070856968", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:29Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:29Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:55Z", "finishedAt": "2020-01-06T22:28:28Z", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:28:40.335 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65 Jan-06 22:28:41.026 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65 { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-d37d730fe8dfbd3d1e26e0d26c301f65", "uid": "6a7712cb-e99b-438f-81bf-55d3026452be", "resourceVersion": "1070857438", "creationTimestamp": "2020-01-06T22:25:52Z", "deletionTimestamp": "2020-01-06T22:28:40Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_7" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.167.38/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-8", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-8", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-08.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:29Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:29Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "67.58.53.168", "podIP": "10.244.167.38", "podIPs": [ { "ip": "10.244.167.38" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-d37d730fe8dfbd3d1e26e0d26c301f65", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:55Z", "finishedAt": "2020-01-06T22:28:28Z", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://e19417b1e847b62307804e0569db232d0c8cdbb5554846c9b93d3fee4da9f22e", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:28:41.427 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: similarity_chunk (Yeast/7); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/d3/7d730fe8dfbd3d1e26e0d26c301f65] Jan-06 22:28:42.320 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:28:43.044 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:43.462 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:28:44.132 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:44.492 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:28:45.123 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070856924", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:28Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:28Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:55Z", "finishedAt": "2020-01-06T22:28:26Z", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:28:45.574 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status Jan-06 22:28:46.240 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a/status", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070856924", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:28Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:28Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:55Z", "finishedAt": "2020-01-06T22:28:26Z", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:28:47.089 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a Jan-06 22:28:47.724 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-5096a67ad37860552fd82c4ed32e8b8a", "uid": "f0fbca7c-a593-4035-bb28-b4193b9bc27b", "resourceVersion": "1070857793", "creationTimestamp": "2020-01-06T22:25:53Z", "deletionTimestamp": "2020-01-06T22:28:47Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_9" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.152.72/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-10", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-10", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-03.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:28Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:28Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "67.58.53.160", "podIP": "10.244.152.72", "podIPs": [ { "ip": "10.244.152.72" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-5096a67ad37860552fd82c4ed32e8b8a", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:55Z", "finishedAt": "2020-01-06T22:28:26Z", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://6199ce1bec29b451e51b5b8839f64df1ae09d8cbb48da31ed032371822cd3c9d", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:28:48.086 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: similarity_chunk (Yeast/9); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/50/96a67ad37860552fd82c4ed32e8b8a] Jan-06 22:28:48.828 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:28:49.452 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:49.818 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:28:50.449 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070857589", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:43Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:43Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:51Z", "finishedAt": "2020-01-06T22:28:42Z", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:28:50.832 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status Jan-06 22:28:51.468 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac/status", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070857589", "creationTimestamp": "2020-01-06T22:25:49Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:43Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:43Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:51Z", "finishedAt": "2020-01-06T22:28:42Z", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:28:52.453 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac Jan-06 22:28:53.104 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e412590737b78f42cd4a9b895e8782ac", "uid": "b1cca8ad-c3ad-4b7e-9968-88155e12fa49", "resourceVersion": "1070858011", "creationTimestamp": "2020-01-06T22:25:49Z", "deletionTimestamp": "2020-01-06T22:28:53Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_0" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.4.17/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-3", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-3", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-chase-ci-04.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:43Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:43Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:49Z" } ], "hostIP": "67.58.53.161", "podIP": "10.244.4.17", "podIPs": [ { "ip": "10.244.4.17" } ], "startTime": "2020-01-06T22:25:49Z", "containerStatuses": [ { "name": "nf-e412590737b78f42cd4a9b895e8782ac", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:51Z", "finishedAt": "2020-01-06T22:28:42Z", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://536c81dd46df35264a47f3dd7a616fcecb1142ff3150b03bd34369e0b730aac8", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:28:53.458 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: similarity_chunk (Yeast/0); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/e4/12590737b78f42cd4a9b895e8782ac] Jan-06 22:28:55.542 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:28:56.190 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:56.553 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:28:57.192 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070848730", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:54Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:57.614 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:28:58.241 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:58.646 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:28:59.336 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070848841", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:55Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "running": { "startedAt": "2020-01-06T22:25:54Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:28:59.703 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:00.461 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:00.827 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:01.455 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:01.860 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:29:02.553 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070858465", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:59Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:59Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:54Z", "finishedAt": "2020-01-06T22:28:58Z", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:29:03.076 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status Jan-06 22:29:03.788 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5/status", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070858465", "creationTimestamp": "2020-01-06T22:25:51Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:59Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:59Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:54Z", "finishedAt": "2020-01-06T22:28:58Z", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:29:04.312 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5 Jan-06 22:29:05.085 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5 { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-8936f53648905107a56f3ff27d4c8fd5", "uid": "78703c61-1a55-445d-bd32-716fe3f1249e", "resourceVersion": "1070858822", "creationTimestamp": "2020-01-06T22:25:51Z", "deletionTimestamp": "2020-01-06T22:29:05Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_5" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.3.6/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-6", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-6", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "k8s-gpu-01.calit2.optiputer.net", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:59Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:28:59Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:51Z" } ], "hostIP": "67.58.53.155", "podIP": "10.244.3.6", "podIPs": [ { "ip": "10.244.3.6" } ], "startTime": "2020-01-06T22:25:51Z", "containerStatuses": [ { "name": "nf-8936f53648905107a56f3ff27d4c8fd5", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:54Z", "finishedAt": "2020-01-06T22:28:58Z", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://912cdfb1800830237352be39da3c0ddef5e22940f7e3cfe1cffac45b96d3892d", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:29:05.486 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: similarity_chunk (Yeast/5); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/89/36f53648905107a56f3ff27d4c8fd5] Jan-06 22:29:06.078 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:29:06.726 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070858738", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:29:03Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:29:03Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:54Z", "finishedAt": "2020-01-06T22:29:02Z", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:29:07.095 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status Jan-06 22:29:07.764 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de/status", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070858738", "creationTimestamp": "2020-01-06T22:25:52Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:29:03Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:29:03Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:54Z", "finishedAt": "2020-01-06T22:29:02Z", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:29:08.433 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de Jan-06 22:29:09.098 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-cfb9ed98e2f7153b5af48207a449b6de", "uid": "bbfb3958-a2b8-4255-ac0b-e0aea2d328cb", "resourceVersion": "1070859089", "creationTimestamp": "2020-01-06T22:25:52Z", "deletionTimestamp": "2020-01-06T22:29:09Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_6" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.37.55/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-9", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-9", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "prp-gpu-4.t2.ucsd.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:29:03Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:29:03Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:52Z" } ], "hostIP": "169.228.132.16", "podIP": "10.244.37.55", "podIPs": [ { "ip": "10.244.37.55" } ], "startTime": "2020-01-06T22:25:52Z", "containerStatuses": [ { "name": "nf-cfb9ed98e2f7153b5af48207a449b6de", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:25:54Z", "finishedAt": "2020-01-06T22:29:02Z", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://00ef8dd1669be72e40ead722026fdbae2da6de0a7c65fb73189075033d5e31b3", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:29:09.568 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: similarity_chunk (Yeast/6); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/cf/b9ed98e2f7153b5af48207a449b6de] Jan-06 22:29:10.393 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:11.045 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:11.480 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:12.112 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:12.483 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:13.156 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:13.713 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:14.468 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:17.483 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:18.164 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:18.593 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:19.418 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:22.483 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:23.307 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:23.830 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:24.583 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:27.483 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:28.180 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:28.650 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:29.443 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:32.484 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:33.170 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:33.643 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:34.432 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:37.484 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:38.172 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:38.612 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:39.298 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:42.485 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:43.165 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:43.874 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:44.599 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:47.486 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:48.166 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:48.575 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:49.245 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:52.487 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:53.189 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:53.737 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:54.539 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:57.487 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:58.183 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:29:58.615 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:29:59.306 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:02.488 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:03.401 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:04.144 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:04.838 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:07.489 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:08.201 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:08.646 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:09.341 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:12.489 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:13.290 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:13.647 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:14.277 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:17.490 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:18.111 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:18.533 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:19.171 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:22.490 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:23.822 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:24.176 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:24.803 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:27.491 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:28.241 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:28.637 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:29.289 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:32.490 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:33.164 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:33.622 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:34.362 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:37.491 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor k8s > tasks to be completed: 1 -- pending tasks are shown below ~> TaskHandler[id: 12; name: similarity_chunk (Yeast/8); status: SUBMITTED; exit: -; error: -; workDir: /workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75] Jan-06 22:30:37.886 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:38.556 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:38.975 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:39.639 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:42.885 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:43.554 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:44.070 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:44.746 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:47.886 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:48.811 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:49.293 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:49.991 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:52.885 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:53.719 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:54.104 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:54.782 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:57.885 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:58.622 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:30:59.076 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:30:59.803 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:31:02.885 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:31:03.526 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:31:03.923 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:31:04.600 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:31:07.886 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:31:08.497 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:31:12.886 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:31:13.150 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:31:17.887 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:31:18.166 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:31:22.888 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:31:23.221 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:31:27.889 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:31:28.156 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:31:32.890 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:31:33.153 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:31:37.890 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:31:38.156 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:31:42.890 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:31:43.165 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070849743", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:26:05Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "running": { "startedAt": "2020-01-06T22:26:04Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:31:47.890 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status Jan-06 22:31:48.155 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75/status", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070868243", "creationTimestamp": "2020-01-06T22:25:53Z", "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:44Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:44Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:26:04Z", "finishedAt": "2020-01-06T22:31:43Z", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:31:49.188 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75 Jan-06 22:31:49.477 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75 { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-28d955cf18e9764e53c797fe53b2bf75", "uid": "7ba49b30-1fbf-4651-b424-bc667d4f21d2", "resourceVersion": "1070868570", "creationTimestamp": "2020-01-06T22:25:53Z", "deletionTimestamp": "2020-01-06T22:31:49Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "similarity_chunk", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_chunk_Yeast_8" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.223.228/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-11", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-11", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "fiona8-3.calit2.uci.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:44Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:44Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:25:53Z" } ], "hostIP": "192.5.19.137", "podIP": "10.244.223.228", "podIPs": [ { "ip": "10.244.223.228" } ], "startTime": "2020-01-06T22:25:53Z", "containerStatuses": [ { "name": "nf-28d955cf18e9764e53c797fe53b2bf75", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:26:04Z", "finishedAt": "2020-01-06T22:31:43Z", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:baf732e37e238d32823dd956abde009a08ea4f65bdc806c9c29cd9c96655241e", "containerID": "docker://0d27c48cfe8db42d3b9061301ed59f7cf1811bace9c8af9ac53e9eafe53d358d", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:31:49.477 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: similarity_chunk (Yeast/8); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/28/d955cf18e9764e53c797fe53b2bf75] Jan-06 22:31:52.107 [Actor Thread 18] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > similarity_merge (Yeast) -- work folder: /workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd Jan-06 22:31:52.249 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "similarity_merge_Yeast", "processName": "similarity_merge", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:31:52.529 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070868732", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Burstable" } } Jan-06 22:31:52.529 [Task submitter] INFO nextflow.Session - [e9/c000de] Submitted process > similarity_merge (Yeast) Jan-06 22:31:52.891 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:31:53.158 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070868738", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-e9c000ded93e303e069f5b358d26eacd]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-e9c000ded93e303e069f5b358d26eacd]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Burstable" } } Jan-06 22:31:57.891 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:31:58.169 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:02.890 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:03.494 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:07.890 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:08.600 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:09.008 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:09.691 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:12.891 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:13.559 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:13.987 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:14.665 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:17.892 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:18.525 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:18.917 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:19.571 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:22.892 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:23.532 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:23.970 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:24.693 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:27.892 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:28.542 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:28.913 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:29.545 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:32.892 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:33.514 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:33.898 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:34.519 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:37.892 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:38.537 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:38.961 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:39.674 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:42.893 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:43.600 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:44.028 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:44.785 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:47.893 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:48.572 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:49.106 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:49.790 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:52.894 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:53.619 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:54.080 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:54.800 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:57.894 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:58.654 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:32:59.128 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:32:59.854 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:02.894 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:03.692 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:04.096 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:04.872 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:07.894 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:08.607 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:09.044 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:09.742 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:12.894 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:13.797 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:14.225 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:14.959 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:17.895 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:18.591 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:19.024 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:19.715 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:22.894 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:23.786 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:24.214 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:24.911 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:27.894 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:28.666 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:29.123 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:29.791 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:32.894 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:33.561 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:33.963 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:34.624 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:37.894 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:38.577 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:38.979 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:39.599 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:42.895 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:43.533 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:43.920 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:44.596 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:47.894 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:48.501 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:52.895 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:53.170 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:33:57.896 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:33:58.160 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:02.897 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:03.161 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:07.898 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:08.161 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:12.898 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:13.174 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:17.898 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:18.171 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:22.898 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:23.184 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:27.899 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:28.231 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:32.898 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:33.171 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:37.899 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:38.582 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:38.977 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:39.672 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:42.899 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:43.560 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:44.067 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:44.731 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:47.900 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:48.770 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:49.329 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:50.177 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:52.900 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:53.613 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:54.186 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:54.921 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:34:57.899 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:34:58.510 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:35:02.899 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:35:03.166 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:35:07.899 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:35:08.163 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070869052", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:57Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "running": { "startedAt": "2020-01-06T22:31:56Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:35:12.899 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status Jan-06 22:35:13.208 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd/status", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070878991", "creationTimestamp": "2020-01-06T22:31:52Z", "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:11Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:11Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:31:56Z", "finishedAt": "2020-01-06T22:35:10Z", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": false } ], "qosClass": "Burstable" } } Jan-06 22:35:13.641 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd Jan-06 22:35:13.916 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-e9c000ded93e303e069f5b358d26eacd", "uid": "e7a91deb-3de2-4db6-99d3-34fb821fec6f", "resourceVersion": "1070879181", "creationTimestamp": "2020-01-06T22:31:52Z", "deletionTimestamp": "2020-01-06T22:35:13Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "similarity_merge", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "similarity_merge_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.20/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-e9c000ded93e303e069f5b358d26eacd; memory limit for container nf-e9c000ded93e303e069f5b358d26eacd", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-12", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-12", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:11Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:11Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:31:52Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.20", "podIPs": [ { "ip": "10.244.14.20" } ], "startTime": "2020-01-06T22:31:52Z", "containerStatuses": [ { "name": "nf-e9c000ded93e303e069f5b358d26eacd", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:31:56Z", "finishedAt": "2020-01-06T22:35:10Z", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://bda4c3a29f6d4fe2128e1fd61bfe5df035c5ebab156ffa892f6e5e29e5a2ec41", "started": false } ], "qosClass": "Burstable" } } Jan-06 22:35:13.916 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: similarity_merge (Yeast); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/e9/c000ded93e303e069f5b358d26eacd] Jan-06 22:35:14.346 [Actor Thread 29] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > threshold (Yeast) -- work folder: /workspace/cole/work/64/b9f750bd901357a8200a021ca3eb34 Jan-06 22:35:14.489 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "threshold_Yeast", "processName": "threshold", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/64/b9f750bd901357a8200a021ca3eb34", "resources": { "limits": { "cpu": 1, "memory": "8192Mi" } }, "volumeMounts": [ { "name": "vol-13", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-13", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:35:14.775 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34", "uid": "05f0200c-15cc-417c-a373-95e47d17e420", "resourceVersion": "1070879236", "creationTimestamp": "2020-01-06T22:35:14Z", "labels": { "app": "nextflow", "processName": "threshold", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "threshold_Yeast" }, "annotations": { "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-13", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/64/b9f750bd901357a8200a021ca3eb34", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-13", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Guaranteed" } } Jan-06 22:35:14.775 [Task submitter] INFO nextflow.Session - [64/b9f750] Submitted process > threshold (Yeast) Jan-06 22:35:17.899 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34/status Jan-06 22:35:18.168 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34/status", "uid": "05f0200c-15cc-417c-a373-95e47d17e420", "resourceVersion": "1070879420", "creationTimestamp": "2020-01-06T22:35:14Z", "labels": { "app": "nextflow", "processName": "threshold", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "threshold_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.243/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-13", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/64/b9f750bd901357a8200a021ca3eb34", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-13", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:14Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:14Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-64b9f750bd901357a8200a021ca3eb34]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:14Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-64b9f750bd901357a8200a021ca3eb34]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:14Z" } ], "hostIP": "129.93.241.2", "startTime": "2020-01-06T22:35:14Z", "containerStatuses": [ { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:35:22.900 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34/status Jan-06 22:35:23.166 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34/status", "uid": "05f0200c-15cc-417c-a373-95e47d17e420", "resourceVersion": "1070879480", "creationTimestamp": "2020-01-06T22:35:14Z", "labels": { "app": "nextflow", "processName": "threshold", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "threshold_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.243/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-13", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/64/b9f750bd901357a8200a021ca3eb34", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-13", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:14Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:18Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:18Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:14Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.243", "podIPs": [ { "ip": "10.244.180.243" } ], "startTime": "2020-01-06T22:35:14Z", "containerStatuses": [ { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "state": { "running": { "startedAt": "2020-01-06T22:35:17Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://257fe6a4abb9aee46ba1c0e7ef4f576a6e05ee54b65b50295167f198ee928935", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:35:27.900 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34/status Jan-06 22:35:28.172 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34/status", "uid": "05f0200c-15cc-417c-a373-95e47d17e420", "resourceVersion": "1070879480", "creationTimestamp": "2020-01-06T22:35:14Z", "labels": { "app": "nextflow", "processName": "threshold", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "threshold_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.243/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-13", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/64/b9f750bd901357a8200a021ca3eb34", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-13", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:14Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:18Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:18Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:14Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.243", "podIPs": [ { "ip": "10.244.180.243" } ], "startTime": "2020-01-06T22:35:14Z", "containerStatuses": [ { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "state": { "running": { "startedAt": "2020-01-06T22:35:17Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://257fe6a4abb9aee46ba1c0e7ef4f576a6e05ee54b65b50295167f198ee928935", "started": true } ], "qosClass": "Guaranteed" } } Jan-06 22:35:32.899 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34/status Jan-06 22:35:33.168 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34/status", "uid": "05f0200c-15cc-417c-a373-95e47d17e420", "resourceVersion": "1070880345", "creationTimestamp": "2020-01-06T22:35:14Z", "labels": { "app": "nextflow", "processName": "threshold", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "threshold_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.243/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-13", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/64/b9f750bd901357a8200a021ca3eb34", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-13", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:14Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:31Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:31Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:14Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.243", "podIPs": [ { "ip": "10.244.180.243" } ], "startTime": "2020-01-06T22:35:14Z", "containerStatuses": [ { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:35:17Z", "finishedAt": "2020-01-06T22:35:30Z", "containerID": "docker://257fe6a4abb9aee46ba1c0e7ef4f576a6e05ee54b65b50295167f198ee928935" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://257fe6a4abb9aee46ba1c0e7ef4f576a6e05ee54b65b50295167f198ee928935", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:35:34.504 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34 Jan-06 22:35:34.812 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34 { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-64b9f750bd901357a8200a021ca3eb34", "uid": "05f0200c-15cc-417c-a373-95e47d17e420", "resourceVersion": "1070880570", "creationTimestamp": "2020-01-06T22:35:14Z", "deletionTimestamp": "2020-01-06T22:35:34Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "threshold", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "threshold_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.180.243/32", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-13", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/64/b9f750bd901357a8200a021ca3eb34", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "cpu": "1", "memory": "8Gi" }, "requests": { "cpu": "1", "memory": "8Gi" } }, "volumeMounts": [ { "name": "vol-13", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "hcc-gpn-k8-1.unl.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:14Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:31Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:31Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:14Z" } ], "hostIP": "129.93.241.2", "podIP": "10.244.180.243", "podIPs": [ { "ip": "10.244.180.243" } ], "startTime": "2020-01-06T22:35:14Z", "containerStatuses": [ { "name": "nf-64b9f750bd901357a8200a021ca3eb34", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:35:17Z", "finishedAt": "2020-01-06T22:35:30Z", "containerID": "docker://257fe6a4abb9aee46ba1c0e7ef4f576a6e05ee54b65b50295167f198ee928935" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://257fe6a4abb9aee46ba1c0e7ef4f576a6e05ee54b65b50295167f198ee928935", "started": false } ], "qosClass": "Guaranteed" } } Jan-06 22:35:34.812 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: threshold (Yeast); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/64/b9f750bd901357a8200a021ca3eb34] Jan-06 22:35:36.128 [Actor Thread 30] TRACE nextflow.k8s.K8sExecutor - [K8s] launching process > extract (Yeast) -- work folder: /workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40 Jan-06 22:35:36.271 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API request POST /api/v1/namespaces/deepgtex-prp/pods { "apiVersion": "v1", "kind": "Pod", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "labels": { "app": "nextflow", "runName": "goofy-bartik", "taskName": "extract_Yeast", "processName": "extract", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0" } }, "spec": { "restartPolicy": "Never", "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" } ] } ], "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } } ] } } Jan-06 22:35:36.547 [Task submitter] TRACE nextflow.k8s.client.K8sClient - [K8s] API response POST /api/v1/namespaces/deepgtex-prp/pods { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070880707", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "qosClass": "Burstable" } } Jan-06 22:35:36.547 [Task submitter] INFO nextflow.Session - [9b/809c25] Submitted process > extract (Yeast) Jan-06 22:35:37.900 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor k8s > tasks to be completed: 1 -- pending tasks are shown below ~> TaskHandler[id: 17; name: extract (Yeast); status: SUBMITTED; exit: -; error: -; workDir: /workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40] Jan-06 22:35:37.900 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:35:38.165 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070880715", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-9b809c250ffba3366c9f41dc005c9a40]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-9b809c250ffba3366c9f41dc005c9a40]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Burstable" } } Jan-06 22:35:42.900 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:35:43.173 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881010", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Pending", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-9b809c250ffba3366c9f41dc005c9a40]" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z", "reason": "ContainersNotReady", "message": "containers with unready status: [nf-9b809c250ffba3366c9f41dc005c9a40]" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "waiting": { "reason": "ContainerCreating" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0-cpu", "imageID": "", "started": false } ], "qosClass": "Burstable" } } Jan-06 22:35:47.901 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:35:48.166 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:35:52.901 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:35:53.166 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:35:57.901 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:35:58.170 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:36:02.901 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:36:03.181 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:36:07.901 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:36:08.168 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:36:12.902 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:36:13.174 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:36:17.901 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:36:18.169 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:36:22.901 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:36:23.176 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:36:27.901 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:36:28.165 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:36:32.901 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:36:33.233 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:36:37.901 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:36:38.171 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:36:42.902 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:36:43.166 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:36:47.902 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:36:48.196 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:36:52.902 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:36:53.172 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070881188", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Running", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" }, { "type": "Ready", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "ContainersReady", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:43Z" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "running": { "startedAt": "2020-01-06T22:35:42Z" } }, "lastState": { }, "ready": true, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": true } ], "qosClass": "Burstable" } } Jan-06 22:36:57.903 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status Jan-06 22:36:58.168 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response GET /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40/status", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070885859", "creationTimestamp": "2020-01-06T22:35:36Z", "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:36:55Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:36:55Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:35:42Z", "finishedAt": "2020-01-06T22:36:54Z", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": false } ], "qosClass": "Burstable" } } Jan-06 22:36:58.666 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API request DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40 Jan-06 22:36:58.957 [Task monitor] TRACE nextflow.k8s.client.K8sClient - [K8s] API response DELETE /api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40 { "kind": "Pod", "apiVersion": "v1", "metadata": { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "namespace": "deepgtex-prp", "selfLink": "/api/v1/namespaces/deepgtex-prp/pods/nf-9b809c250ffba3366c9f41dc005c9a40", "uid": "d50a2af3-1591-46b9-8c49-017435b16ef4", "resourceVersion": "1070886076", "creationTimestamp": "2020-01-06T22:35:36Z", "deletionTimestamp": "2020-01-06T22:36:58Z", "deletionGracePeriodSeconds": 0, "labels": { "app": "nextflow", "processName": "extract", "runName": "goofy-bartik", "sessionId": "uuid-c54aeda8-b621-435b-bff2-78db026e8ab0", "taskName": "extract_Yeast" }, "annotations": { "cni.projectcalico.org/podIP": "10.244.14.8/32", "kubernetes.io/limit-ranger": "LimitRanger plugin set: memory request for container nf-9b809c250ffba3366c9f41dc005c9a40; memory limit for container nf-9b809c250ffba3366c9f41dc005c9a40", "kubernetes.io/psp": "nautilususerpolicy" } }, "spec": { "volumes": [ { "name": "vol-14", "persistentVolumeClaim": { "claimName": "deepgtex-prp" } }, { "name": "default-token-fj9lc", "secret": { "secretName": "default-token-fj9lc", "defaultMode": 420 } } ], "containers": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "image": "systemsgenetics/kinc:3.3.0-cpu", "command": [ "/bin/bash", "-ue", ".command.run" ], "workingDir": "/workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40", "env": [ { "name": "NVIDIA_VISIBLE_DEVICES", "value": "none" } ], "resources": { "limits": { "memory": "4Gi" }, "requests": { "memory": "256Mi" } }, "volumeMounts": [ { "name": "vol-14", "mountPath": "/workspace" }, { "name": "default-token-fj9lc", "readOnly": true, "mountPath": "/var/run/secrets/kubernetes.io/serviceaccount" } ], "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "imagePullPolicy": "IfNotPresent", "securityContext": { "allowPrivilegeEscalation": false } } ], "restartPolicy": "Never", "terminationGracePeriodSeconds": 30, "dnsPolicy": "ClusterFirst", "serviceAccountName": "default", "serviceAccount": "default", "nodeName": "ps-100g.sdsu.edu", "securityContext": { }, "affinity": { "nodeAffinity": { "requiredDuringSchedulingIgnoredDuringExecution": { "nodeSelectorTerms": [ { "matchExpressions": [ { "key": "env", "operator": "In", "values": [ "production" ] } ] } ] } } }, "schedulerName": "default-scheduler", "tolerations": [ { "key": "node.kubernetes.io/not-ready", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "node.kubernetes.io/unreachable", "operator": "Exists", "effect": "NoExecute", "tolerationSeconds": 300 }, { "key": "nautilus.io/chase-ci", "operator": "Exists", "effect": "NoSchedule" } ], "priority": 0, "enableServiceLinks": true }, "status": { "phase": "Succeeded", "conditions": [ { "type": "Initialized", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z", "reason": "PodCompleted" }, { "type": "Ready", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:36:55Z", "reason": "PodCompleted" }, { "type": "ContainersReady", "status": "False", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:36:55Z", "reason": "PodCompleted" }, { "type": "PodScheduled", "status": "True", "lastProbeTime": null, "lastTransitionTime": "2020-01-06T22:35:36Z" } ], "hostIP": "130.191.103.1", "podIP": "10.244.14.8", "podIPs": [ { "ip": "10.244.14.8" } ], "startTime": "2020-01-06T22:35:36Z", "containerStatuses": [ { "name": "nf-9b809c250ffba3366c9f41dc005c9a40", "state": { "terminated": { "exitCode": 0, "reason": "Completed", "startedAt": "2020-01-06T22:35:42Z", "finishedAt": "2020-01-06T22:36:54Z", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2" } }, "lastState": { }, "ready": false, "restartCount": 0, "image": "systemsgenetics/kinc:3.3.0", "imageID": "docker-pullable://systemsgenetics/kinc@sha256:2bab0e0ea2e920554ef1f4798897225f7545e65eac1df4fa854edb0852a69e92", "containerID": "docker://b8d5c5fd45d7e1f850a09446e325bc0ee08e30aa09038b9c7afe50cbd3600fa2", "started": false } ], "qosClass": "Burstable" } } Jan-06 22:36:58.958 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: extract (Yeast); status: COMPLETED; exit: 0; error: -; workDir: /workspace/cole/work/9b/809c250ffba3366c9f41dc005c9a40] Jan-06 22:36:59.368 [main] DEBUG nextflow.Session - Session await > all process finished Jan-06 22:36:59.807 [main] DEBUG nextflow.Session - Session await > all barriers passed Jan-06 22:36:59.812 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=14; failedCount=0; ignoredCount=0; cachedCount=0; succeedDuration=31m 37s; failedDuration=0ms; cachedDuration=0ms] Jan-06 22:36:59.812 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file Jan-06 22:36:59.815 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report 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