Apr-19 04:57:50.338 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/scrnaseq -r 1.1.0 --input samplesheet.csv --fasta GRCh38.primary_assembly.genome.fa --gtf gencode.v39.primary_assembly.annotation.gtf -profile singularity -c custom_profile.conf Apr-19 04:57:50.411 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.10.0 Apr-19 04:57:51.788 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/scrnaseq.git Apr-19 04:57:51.807 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/scrnaseq.git Apr-19 04:57:52.064 [main] INFO nextflow.cli.CmdRun - Launching `nf-core/scrnaseq` [shrivelled_ampere] - revision: f31b12f790 [1.1.0] Apr-19 04:57:52.874 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/nextflow.config Apr-19 04:57:52.879 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /data/scRNA/custom_profile.conf Apr-19 04:57:52.879 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/nextflow.config Apr-19 04:57:52.879 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/scRNA/custom_profile.conf Apr-19 04:57:52.892 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity` Apr-19 04:57:53.324 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager Apr-19 04:57:53.339 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Apr-19 04:57:53.340 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Apr-19 04:57:53.345 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Apr-19 04:57:53.858 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity` Apr-19 04:57:53.894 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, genotoul, alice, uppmax, abims, nihbiowulf, nu_genomics, oist, sahmri, mpcdf, leicester, lugh, cambridge, unibe_ibu, vai, podman, czbiohub_aws, jax, cheaha, ccga_med, test, google, computerome, test_kallisto, seg_globe, sanger, pasteur, test_full, eddie, azurebatch, bi, bigpurple, docker, gis, eva, utd_ganymede, charliecloud, fgcz, conda, singularity, icr_davros, munin, rosalind, prince, hasta, hebbe, cfc, utd_sysbio, uzh, debug, genouest, cbe, ebc, ccga_dx, crick, slurm, marvin, phoenix, biohpc_gen, shifter, awsbatch, uct_hpc, imperial, maestro, aws_tower, binac] Apr-19 04:57:53.928 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/ubuntu/.nextflow/plugins Apr-19 04:57:53.929 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Apr-19 04:57:53.932 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Apr-19 04:57:53.932 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Apr-19 04:57:53.933 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Apr-19 04:57:53.940 [main] INFO org.pf4j.AbstractPluginManager - No plugins Apr-19 04:57:53.984 [main] DEBUG nextflow.Session - Session uuid: 573d56f2-660a-430c-afc1-735653d63dba Apr-19 04:57:53.984 [main] DEBUG nextflow.Session - Run name: shrivelled_ampere Apr-19 04:57:53.985 [main] DEBUG nextflow.Session - Executor pool size: 8 Apr-19 04:57:54.011 [main] DEBUG nextflow.cli.CmdRun - Version: 21.10.0 build 5640 Created: 11-11-2021 18:27 UTC System: Linux 5.4.0-90-generic Runtime: Groovy 3.0.9 on OpenJDK 64-Bit Server VM 11.0.14.1+1-Ubuntu-0ubuntu1.20.04 Encoding: UTF-8 (UTF-8) Process: 543970@sarahtest [127.0.1.1] CPUs: 8 - Mem: 31.4 GB (5.8 GB) - Swap: 0 (0) Apr-19 04:57:54.061 [main] DEBUG nextflow.Session - Work-dir: /data/scRNA/work [ext2/ext3] Apr-19 04:57:54.090 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Apr-19 04:57:54.099 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Apr-19 04:57:54.195 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 Apr-19 04:57:54.461 [main] DEBUG nextflow.Session - Session start invoked Apr-19 04:57:54.467 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /data/scRNA/results/pipeline_info/execution_trace.txt Apr-19 04:57:54.478 [main] DEBUG nextflow.Session - Using default localLib path: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/lib Apr-19 04:57:54.482 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/lib Apr-19 04:57:54.483 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/lib/nfcore_external_java_deps.jar Apr-19 04:57:56.724 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Apr-19 04:57:56.741 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/scrnaseq v1.1.0 ------------------------------------------------------ Apr-19 04:57:56.961 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 Apr-19 04:57:57.055 [main] INFO nextflow.Nextflow - Core Nextflow options revision : 1.1.0 runName : shrivelled_ampere containerEngine : singularity container : nfcore/scrnaseq:1.1.0 launchDir : /data/scRNA workDir : /data/scRNA/work projectDir : /home/ubuntu/.nextflow/assets/nf-core/scrnaseq userName : ubuntu profile : singularity configFiles : /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/nextflow.config, /data/scRNA/custom_profile.conf Input/output options input : samplesheet.csv input_paths : null email : false Mandatory arguments barcode_whitelist : false Reference genome options genome : false fasta : GRCh38.primary_assembly.genome.fa transcript_fasta : false gtf : gencode.v39.primary_assembly.annotation.gtf save_reference : false Alevin Options salmon_index : false txp2gene : false STARSolo Options star_index : false Kallisto/BUS Options kallisto_gene_map : false bustools_correct : true kallisto_index : false Generic options email_on_fail : false max_multiqc_email_size : 25 MB multiqc_config : false Max job request options max_cpus : 8 max_memory : 28 GB max_time : 16h Institutional config options config_profile_name : false config_profile_description: Profile for Zeus use at The Pawsey Supercomputing Research Centre, Australia. Current until new Setonix system is deployed. config_profile_contact : Sarah Beecroft (@SarahBeecroft) config_profile_url : https://pawsey.org.au [Only displaying parameters that differ from pipeline default] ------------------------------------------------------ ------------------------------------------------------ Apr-19 04:57:57.122 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.122 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.127 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Apr-19 04:57:57.132 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=31.4 GB; capacity=8; pollInterval=100ms; dumpInterval=5m Apr-19 04:57:57.211 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.211 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.225 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.225 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.248 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:low_memory` matches labels `low_memory` for process with name build_salmon_index Apr-19 04:57:57.249 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.250 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:high_memory` matches labels `high_memory` for process with name makeSTARindex Apr-19 04:57:57.264 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.264 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.276 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mid_memory` matches labels `mid_memory` for process with name build_kallisto_index Apr-19 04:57:57.276 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.276 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.292 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.293 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.300 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.300 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.305 [Actor Thread 2] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=docker://nfcore/scrnaseq:1.1.0; path=/data/singularity/cache/nfcore-scrnaseq-1.1.0.img Apr-19 04:57:57.331 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:high_memory` matches labels `high_memory` for process with name alevin Apr-19 04:57:57.332 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.332 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.349 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.349 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.356 [Actor Thread 8] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/assets/whitelist/10x_V3_barcode_whitelist.txt.gz Apr-19 04:57:57.379 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:high_memory` matches labels `high_memory` for process with name star Apr-19 04:57:57.380 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.380 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.392 [Actor Thread 7] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/bin/scrape_software_versions.py Apr-19 04:57:57.410 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mid_memory` matches labels `mid_memory` for process with name kallisto Apr-19 04:57:57.411 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.411 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.416 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mid_memory` matches labels `mid_memory` for process with name bustools_correct_sort Apr-19 04:57:57.417 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.417 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.423 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mid_memory` matches labels `mid_memory` for process with name bustools_count Apr-19 04:57:57.424 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.424 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.431 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.432 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.458 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.458 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.470 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Apr-19 04:57:57.470 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Apr-19 04:57:57.479 [Actor Thread 3] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/docs/output.md Apr-19 04:57:57.481 [Actor Thread 3] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/docs/images/nf-core-scrnaseq_logo.png Apr-19 04:57:57.481 [Actor Thread 3] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/docs/images/nfcore-scrnaseq_logo.png Apr-19 04:57:57.481 [Actor Thread 3] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/bin/markdown_to_html.py Apr-19 04:57:57.483 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: bustools_count, extract_transcriptome, star, output_documentation, alevin, makeSTARindex, alevin_qc, build_salmon_index, build_kallisto_index, kallisto, bustools_inspect, build_gene_map, build_txp2gene, unzip_10x_barcodes, bustools_correct_sort, get_software_versions, multiqc Apr-19 04:57:57.484 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Apr-19 04:57:57.484 [main] DEBUG nextflow.Session - Session await Apr-19 04:57:57.591 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Apr-19 04:57:57.597 [Task submitter] INFO nextflow.Session - [00/5bce91] Submitted process > unzip_10x_barcodes (V3) Apr-19 04:57:57.613 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Apr-19 04:57:57.614 [Task submitter] INFO nextflow.Session - [d0/70bcbb] Submitted process > build_txp2gene (gencode.v39.primary_assembly.annotation.gtf) Apr-19 04:57:57.624 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Apr-19 04:57:57.626 [Task submitter] INFO nextflow.Session - [b6/b63d6b] Submitted process > get_software_versions Apr-19 04:57:57.643 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Apr-19 04:57:57.644 [Task submitter] INFO nextflow.Session - [c4/963d65] Submitted process > output_documentation Apr-19 04:57:57.673 [Actor Thread 19] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.0 s; external sort time: 0.002 s; total time: 0.002 s Apr-19 04:57:57.674 [Actor Thread 19] DEBUG nextflow.file.FileCollector - >> temp file exists? false Apr-19 04:57:57.674 [Actor Thread 19] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /tmp/10eb154225e7477603911f0d79b809a0.collect-file Apr-19 04:57:57.741 [Actor Thread 19] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/10eb154225e7477603911f0d79b809a0.collect-file Apr-19 04:57:57.751 [Actor Thread 19] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-10850129682399868885 Apr-19 04:57:58.593 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: output_documentation; status: COMPLETED; exit: 0; error: -; workDir: /data/scRNA/work/c4/963d659f45c39f2a22eb8134884ef8] Apr-19 04:57:58.600 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Apr-19 04:57:58.606 [Task submitter] INFO nextflow.Session - [45/089d38] Submitted process > extract_transcriptome (GRCh38.primary_assembly.genome.fa) Apr-19 04:57:58.612 [Task monitor] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=24; maxQueueSize=72; keepAlive=1m Apr-19 04:57:58.689 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: unzip_10x_barcodes (V3); status: COMPLETED; exit: 0; error: -; workDir: /data/scRNA/work/00/5bce915dcbc2ed7606ee05f380366a] Apr-19 04:57:59.481 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: get_software_versions; status: COMPLETED; exit: 0; error: -; workDir: /data/scRNA/work/b6/b63d6b8d8e0f420eaab182babd8284] Apr-19 04:58:03.510 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: build_txp2gene (gencode.v39.primary_assembly.annotation.gtf); status: COMPLETED; exit: 0; error: -; workDir: /data/scRNA/work/d0/70bcbbebc38d22f00fbe3ec954ee3f] Apr-19 04:58:51.674 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: extract_transcriptome (GRCh38.primary_assembly.genome.fa); status: COMPLETED; exit: 0; error: -; workDir: /data/scRNA/work/45/089d3815e85323f26f69fff55d963e] Apr-19 04:58:51.696 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Apr-19 04:58:51.697 [Task submitter] INFO nextflow.Session - [08/e2783a] Submitted process > build_salmon_index (GRCh38.primary_assembly.genome.fa.transcriptome.fa) Apr-19 05:02:56.763 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: build_salmon_index (GRCh38.primary_assembly.genome.fa.transcriptome.fa); status: COMPLETED; exit: 0; error: -; workDir: /data/scRNA/work/08/e2783ae27b4685e4476899f9d5404f] Apr-19 05:02:56.795 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Apr-19 05:02:56.795 [Task submitter] INFO nextflow.Session - [e0/eba582] Submitted process > alevin (samplesheet) Apr-19 05:02:57.265 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 10; name: alevin (samplesheet); status: RUNNING; exit: -; error: -; workDir: /data/scRNA/work/e0/eba5822f275115d6280ac19ea3dd9f] Apr-19 05:02:57.788 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: alevin (samplesheet); status: COMPLETED; exit: 139; error: -; workDir: /data/scRNA/work/e0/eba5822f275115d6280ac19ea3dd9f] Apr-19 05:02:57.800 [Task monitor] INFO nextflow.processor.TaskProcessor - [e0/eba582] NOTE: Process `alevin (samplesheet)` terminated with an error exit status (139) -- Execution is retried (1) Apr-19 05:02:57.814 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Apr-19 05:02:57.814 [Task submitter] INFO nextflow.Session - [ef/ede980] Re-submitted process > alevin (samplesheet) Apr-19 05:02:58.768 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: alevin (samplesheet); status: COMPLETED; exit: 139; error: -; workDir: /data/scRNA/work/ef/ede980471e1c5ca38793699d1d07a4] Apr-19 05:02:58.787 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'alevin (samplesheet)' Caused by: Process `alevin (samplesheet)` terminated with an error exit status (139) Command executed: salmon alevin -l ISR -1 samplesheet.csv -2 null --chromium -i salmon_index -o samplesheet_alevin_results -p 8 --tgMap txp2gene.tsv --dumpFeatures –-dumpMtx Command exit status: 139 Command output: (empty) Command error: Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### Sign up for the salmon mailing list to hear about new versions, features and updates at: https://oceangenomics.com/subscribe ###Logs will be written to samplesheet_alevin_results/logs [2022-04-19 05:02:58.117] [jointLog] [info] setting maxHashResizeThreads to 8 [2022-04-19 05:02:58.117] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2022-04-19 05:02:58.117] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation. [2022-04-19 05:02:58.117] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2022-04-19 05:02:58.117] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. [2022-04-19 05:02:58.117] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35. [2022-04-19 05:02:58.117] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin Using default value of 0.6 for consensusSlack in Alevin [2022-04-19 05:02:58.297] [alevinLog] [info] Found 243575 transcripts(+0 decoys, +41 short and +0 duplicate names in the index) [2022-04-19 05:02:58.486] [alevinLog] [info] Filled with 243616 txp to gene entries [2022-04-19 05:02:58.538] [alevinLog] [info] Found all transcripts to gene mappings ### alevin (dscRNA-seq quantification) v1.4.0 ### [ program ] => salmon ### [ command ] => alevin ### [ libType ] => { ISR } ### [ mates1 ] => { samplesheet.csv } ### [ mates2 ] => { null } ### [ chromium ] => { } ### [ index ] => { salmon_index } ### [ output ] => { samplesheet_alevin_results } ### [ threads ] => { 8 } ### [ tgMap ] => { txp2gene.tsv } ### [ dumpFeatures ] => { } ### [ ] => { –-dumpMtx } .command.sh: line 2: 551040 Segmentation fault (core dumped) salmon alevin -l ISR -1 samplesheet.csv -2 null --chromium -i salmon_index -o samplesheet_alevin_results -p 8 --tgMap txp2gene.tsv --dumpFeatures –-dumpMtx Work dir: /data/scRNA/work/ef/ede980471e1c5ca38793699d1d07a4 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` Apr-19 05:02:58.793 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `alevin (samplesheet)` terminated with an error exit status (139) Apr-19 05:02:58.814 [Task monitor] DEBUG nextflow.Session - The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) bound ; channel: multiqc_config port 1: (value) bound ; channel: software_versions/* port 2: (queue) closed; channel: workflow_summary port 3: (value) bound ; channel: STAR/* port 4: (value) bound ; channel: alevin/* port 5: (value) bound ; channel: kallisto/* port 6: (cntrl) - ; channel: $ Apr-19 05:02:58.819 [Actor Thread 6] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ubuntu/.nextflow/assets/nf-core/scrnaseq/assets/multiqc_config.yaml Apr-19 05:02:58.829 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below ~> TaskHandler[id: 12; name: multiqc (1); status: NEW; exit: -; error: -; workDir: /data/scRNA/work/57/dd8de31a0ebd40fd450d0a67262b13] Apr-19 05:02:58.844 [main] DEBUG nextflow.Session - Session await > all process finished Apr-19 05:02:58.846 [main] DEBUG nextflow.Session - Session await > all barriers passed Apr-19 05:02:58.960 [main] INFO nextflow.Nextflow - -[nf-core/scrnaseq] Pipeline completed with errors- Apr-19 05:02:58.965 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=6; failedCount=2; ignoredCount=0; cachedCount=0; pendingCount=1; submittedCount=0; runningCount=0; retriesCount=1; abortedCount=0; succeedDuration=17m 19s; failedDuration=14.4s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=4; peakCpus=8; peakMemory=28 GB; ] Apr-19 05:02:58.965 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file Apr-19 05:02:58.967 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report Apr-19 05:02:59.013 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: 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required to install Graphviz -- See http://www.graphviz.org for more info. Apr-19 05:02:59.587 [main] DEBUG nextflow.CacheDB - Closing CacheDB done Apr-19 05:02:59.597 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye