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pident length gapopen qstart qend sstart send evalue bitscore\\\" -mt_mode 1 -taxidlist taxidlist.txt; TIME=\\\"${DATE_NOW} run start 000 blastn nt %e %U %S %P\\\" \\\\time -o ${BLAST_RUNTIME} blastn -db nt -query /blast/blastdb/batch_000.fa -out /blast/results/batch_000-blastn-nt.out -num_threads 15 -task blastn-fast -evalue 1e-3 -outfmt \\\"6 qseqid sacc pident length gapopen qstart qend sstart send evalue bitscore\\\" -mt_mode 1 -taxidlist taxidlist.txt 2\\u003e$ERROR_FILE; BLAST_EXIT_CODE=$?; end=`date +%s`; cat $ERROR_FILE; printf 'RUNTIME %s %f seconds\\\\n' \\\"blast-job-000\\\" $(($end-$start)); echo run end 000 ${BLAST_EXIT_CODE}; echo `date -u +%s%N` run exitCode 000 ${BLAST_EXIT_CODE}\\u003e\\u003e ${BLAST_RUNTIME}; echo `date -u +%s%N` run end 000\\u003e\\u003e ${BLAST_RUNTIME}; gzip /blast/results/batch_000-blastn-nt.out; cp $BLAST_RUNTIME /blast/results/BLAST_RUNTIME-000.out; echo $BLAST_EXIT_CODE \\u003e /blast/results/BLAST_EXIT_CODE.out; if [[ $BLAST_EXIT_CODE -ne 0 ]] ; then if ! gsutil -q stat gs://xxx/metadata/FAILURE.txt ; then gsutil -mq cp $ERROR_FILE gs://dan-mak-xxx/metadata/FAILURE.txt; fi; fi;\"],\"command\":[\"/bin/bash\",\"-c\"],\"env\":[{\"name\":\"BLAST_USAGE_REPORT\",\"value\":\"true\"},{\"name\":\"BLAST_ELB_JOB_ID\",\"value\":\"c00e88115a534168bef06dcfb3469cd2\"},{\"name\":\"BLAST_ELB_BATCH_NUM\",\"value\":\"0\"}],\"image\":\"gcr.io/ncbi-sandbox-blast/ncbi/elb:1.1.3\",\"name\":\"blast\",\"resources\":{\"limits\":{\"cpu\":15,\"memory\":\"510G\"},\"requests\":{\"cpu\":15,\"memory\":\"0.5G\"}},\"volumeMounts\":[{\"mountPath\":\"/blast/blastdb\",\"name\":\"blast-dbs\",\"readOnly\":true},{\"mountPath\":\"/blast/results\",\"name\":\"shared-data\"}],\"workingDir\":\"/blast/blastdb\"},{\"args\":[\"until [ -s /result/BLAST_EXIT_CODE.out ] ; do sleep 1; done; set -ex; ls -1f /result/BLASTDB_LENGTH.out | gsutil -qm cp -I gs://dan-mak-xxx/metadata/; gsutil -mq cp /result/BLAST_RUNTIME-000.out gs://dan-mak-xxx/logs/; gsutil -mq cp 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"terminationMessagePolicy": "File", "volumeMounts": [ { "mountPath": "/result", "name": "shared-data" } ] } ], "dnsPolicy": "ClusterFirst", "initContainers": [ { "args": [ "echo \"BASH version ${BASH_VERSION}\"; start=`date +%s`; log() { ts=`date +'%F %T'`; printf '%s RUNTIME %s %f seconds\\n' \"$ts\" \"$1\" \"$2\"; }; blastdb_path -dbtype nucl -db nt -getvolumespath | tr ' ' '\\n' | parallel vmtouch -tqm 5G; exit_code=$?; end=`date +%s`; log \"cache-blastdbs-to-ram\" $(($end-$start)); exit $exit_code;" ], "command": [ "/bin/bash", "-co", "pipefail" ], "image": "gcr.io/ncbi-sandbox-blast/ncbi/elb:1.1.3", "imagePullPolicy": "IfNotPresent", "name": "load-blastdb-into-ram", "resources": {}, "terminationMessagePath": "/dev/termination-log", "terminationMessagePolicy": "File", "volumeMounts": [ { "mountPath": "/blast/blastdb", "name": "blast-dbs", "readOnly": true } ], "workingDir": "/blast/blastdb" } ], "restartPolicy": "OnFailure", "schedulerName": "default-scheduler", "securityContext": 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"name": "elb-janitor-28046515", "namespace": "default", "ownerReferences": [ { "apiVersion": "batch/v1", "blockOwnerDeletion": true, "controller": true, "kind": "CronJob", "name": "elb-janitor", "uid": "9dcb75a5-ecfa-433b-9a99-7a158fd89f23" } ], "resourceVersion": "11519", "uid": "1ec93ada-e33f-42c0-9c8e-666e1f2a07b7" }, "spec": { "backoffLimit": 6, "completionMode": "NonIndexed", "completions": 1, "parallelism": 1, "selector": { "matchLabels": { "controller-uid": "1ec93ada-e33f-42c0-9c8e-666e1f2a07b7" } }, "suspend": false, "template": { "metadata": { "creationTimestamp": null, "labels": { "app": "janitor", "controller-uid": "1ec93ada-e33f-42c0-9c8e-666e1f2a07b7", "job-name": "elb-janitor-28046515" } }, "spec": { "containers": [ { "env": [ { "name": "ELB_GCP_PROJECT", "value": "my-project-xxx" }, { "name": "ELB_GCP_REGION", "value": "us-west3" }, { "name": "ELB_GCP_ZONE", "value": "us-west3-c" }, { "name": "ELB_RESULTS", "value": "gs://dan-mak-xxx" }, { "name": "ELB_CLUSTER_NAME", 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"job-name": "elb-janitor-28046520" }, "name": "elb-janitor-28046520", "namespace": "default", "ownerReferences": [ { "apiVersion": "batch/v1", "blockOwnerDeletion": true, "controller": true, "kind": "CronJob", "name": "elb-janitor", "uid": "9dcb75a5-ecfa-433b-9a99-7a158fd89f23" } ], "resourceVersion": "13798", "uid": "1413c4c0-31bb-40e3-817c-186e28084073" }, "spec": { "backoffLimit": 6, "completionMode": "NonIndexed", "completions": 1, "parallelism": 1, "selector": { "matchLabels": { "controller-uid": "1413c4c0-31bb-40e3-817c-186e28084073" } }, "suspend": false, "template": { "metadata": { "creationTimestamp": null, "labels": { "app": "janitor", "controller-uid": "1413c4c0-31bb-40e3-817c-186e28084073", "job-name": "elb-janitor-28046520" } }, "spec": { "containers": [ { "env": [ { "name": "ELB_GCP_PROJECT", "value": "my-project-xxx" }, { "name": "ELB_GCP_REGION", "value": "us-west3" }, { "name": "ELB_GCP_ZONE", "value": "us-west3-c" }, { "name": "ELB_RESULTS", "value": 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"{\"apiVersion\":\"batch/v1\",\"kind\":\"Job\",\"metadata\":{\"annotations\":{},\"labels\":{\"app\":\"submit\"},\"name\":\"submit-jobs\",\"namespace\":\"default\"},\"spec\":{\"backoffLimit\":0,\"template\":{\"metadata\":{\"labels\":{\"app\":\"submit\"}},\"spec\":{\"containers\":[{\"env\":[{\"name\":\"ELB_GCP_PROJECT\",\"value\":\"my-project-xxx\"},{\"name\":\"ELB_GCP_ZONE\",\"value\":\"us-west3-c\"},{\"name\":\"ELB_RESULTS\",\"value\":\"gs://dan-xxx\"},{\"name\":\"ELB_CLUSTER_NAME\",\"value\":\"elastic-blast\"},{\"name\":\"ELB_NUM_NODES\",\"value\":\"1\"},{\"name\":\"ELB_PD_SIZE\",\"value\":\"300Gi\"},{\"name\":\"ELB_LABELS\",\"value\":\"cluster-name=elastic-blast,client-hostname=cs-619646043697-default,project=elastic-blast,billingcode=elastic-blast,creator=mohammadmafakheri69,created=2023-04-29-17-32-05,owner=user,program=blastn,db=nt,name=elastic-blast,results=gs---dan-xxx,version=1-0-0\"},{\"name\":\"ELB_USE_LOCAL_SSD\",\"value\":\"false\"}],\"image\":\"gcr.io/ncbi-sandbox-blast/ncbi/elasticblast-job-submit:3.0.0\",\"imagePullPolicy\":\"IfNotPresent\",\"name\":\"submit-jobs\",\"volumeMounts\":[{\"mountPath\":\"/workspace\",\"name\":\"workspace\"}],\"workingDir\":\"/workspace\"}],\"restartPolicy\":\"Never\",\"volumes\":[{\"emptyDir\":{},\"name\":\"workspace\"}]}}}}\n" }, "creationTimestamp": "2023-04-29T17:37:51Z", "generation": 1, "labels": { "app": "submit" }, "name": "submit-jobs", "namespace": "default", "resourceVersion": "12639", "uid": "832c4270-5188-4fea-83b9-e24748790278" }, "spec": { "backoffLimit": 0, "completionMode": "NonIndexed", "completions": 1, "parallelism": 1, "selector": { "matchLabels": { "controller-uid": "832c4270-5188-4fea-83b9-e24748790278" } }, "suspend": false, "template": { "metadata": { "creationTimestamp": null, "labels": { "app": "submit", "controller-uid": "832c4270-5188-4fea-83b9-e24748790278", "job-name": "submit-jobs" } }, "spec": { "containers": [ { "env": [ { "name": "ELB_GCP_PROJECT", "value": "my-project-xxxx" }, { "name": "ELB_GCP_ZONE", "value": "us-west3-c" }, { "name": "ELB_RESULTS", "value": "gs://dan-mak-xxx" }, { "name": "ELB_CLUSTER_NAME", "value": "elastic-blast" }, { "name": "ELB_NUM_NODES", "value": "1" }, { "name": "ELB_PD_SIZE", "value": "300Gi" }, { "name": "ELB_LABELS", "value": 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