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GEMMAKER not writing results after very quick run time on Clemson Palmetto cluster #277

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feltus opened this issue Feb 23, 2023 · 2 comments
Open

GEMMAKER not writing results after very quick run time on Clemson Palmetto cluster #277

feltus opened this issue Feb 23, 2023 · 2 comments
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@spficklin @feltus @JohnHadish
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@feltus
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feltus commented Feb 23, 2023

Description of the bug

My students and I are having several issues with GEMmaker on our cluster. The most important and consistent issue is GEMMaker is running through the workflow VERY QUICKLY and quitting without writing results. It is happening with SRA pulls and with the test run like this:

module add openjdk/11.0.15_10-gcc/9.5.0
nextflow pull systemsgenetics/gemmaker
nextflow run systemsgenetics/gemmaker -profile test,singularity

OR if I do a 'real' rn like this:

extflow run systemsgenetics/gemmaker -profile singularity \

--pipeline kallisto
--kallisto_index_path Arabidopsis_thaliana.TAIR10.cdna.all.fa.indexed
--sras SRAs.txt

Error and .nexftflow.log below.

Command used and terminal output

[ffeltus@node0578 athtest]$ module add openjdk/11.0.15_10-gcc/9.5.0
[ffeltus@node0578 athtest]$ nextflow pull systemsgenetics/gemmaker
Checking systemsgenetics/gemmaker ...
 Already-up-to-date - revision: c7fe33612e [master]
[ffeltus@node0578 athtest]$ nextflow run systemsgenetics/gemmaker -profile singularity \
> --pipeline kallisto \
> --kallisto_index_path Arabidopsis_thaliana.TAIR10.cdna.all.fa.indexed \
> --sras SRAs.txt
N E X T F L O W  ~  version 22.10.7
Launching `https://github.com/systemsgenetics/gemmaker` [berserk_volta] DSL2 - revision: c7fe33612e [master]


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  systemsgenetics/gemmaker v2.1.1
------------------------------------------------------
Core Nextflow options
  revision                  : master
  runName                   : berserk_volta
  containerEngine           : singularity
  launchDir                 : /home/ffeltus/athtest
  workDir                   : /home/ffeltus/athtest/work
  projectDir                : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker
  userName                  : ffeltus
  profile                   : singularity
  configFiles               : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/nextflow.config

Input/output options
  sras                      : SRAs.txt
  failed_run_report_template: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/failed_sra_runs.template.html
  multiqc_config_file       : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/multiqc_config.yaml
  multiqc_custom_logo       : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/systemsgenetics-gemmaker_logo.png

Kallisto Pipeline
  kallisto_index_path       : Arabidopsis_thaliana.TAIR10.cdna.all.fa.indexed
  kallisto_bootstrap_samples: 0

Reference genome options
  igenomes_ignore           : true

Generic options
  publish_dir_mode          : link

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use systemsgenetics/gemmaker for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.3620945

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/systemsgenetics/gemmaker/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (18)
[-        ] process > GEMmaker:get_software_versions     -
[40/3d215c] process > GEMmaker:retrieve_sra_metadata     [100%] 1 of 1 ?
[3e/bb9a5c] process > GEMmaker:download_runs (SRX398820) [100%] 8 of 8 ?
[-        ] process > GEMmaker:fastq_dump                -
[-        ] process > GEMmaker:fastq_merge               -
[-        ] process > GEMmaker:fastqc_1                  -
[-        ] process > GEMmaker:kallisto                  -
[-        ] process > GEMmaker:kallisto_tpm              -
[b4/2401bb] process > GEMmaker:next_sample (SRX398821)   [100%] 8 of 8 ?
[-        ] process > GEMmaker:multiqc                   -
[-        ] process > GEMmaker:create_gem                -
[30/2cc3e0] process > GEMmaker:failed_run_report         [100%] 1 of 1 ?
[-        ] process > GEMmaker:clean_work_files          -
[-        ] process > GEMmaker:clean_work_dirs           -
Pulling Singularity image docker://systemsgenetics/gemmaker:2.1.0 [cache /home/ffeltus/athtest/work/singularity/systemsgenetics-gemmaker-2.1.0.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /home/ffeltus/athtest/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location

[ffeltus@node0578 athtest]$ ls results/
pipeline_info  reports  Samples
[ffeltus@node0578 athtest]$ cat .nextflow.log
Feb-23 11:52:27.778 [main] DEBUG nextflow.cli.Launcher - $> nextflow run systemsgenetics/gemmaker -profile singularity --pipeline kallisto --kallisto_index_path Arabidopsis_thaliana.TAIR10.cdna.all.fa.indexed --sras SRAs.txt
Feb-23 11:52:27.844 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 22.10.7
Feb-23 11:52:27.870 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/ffeltus/.nextflow/plugins; core-plugins: nf-amazon@1.11.4,nf-azure@0.14.2,nf-codecommit@0.1.2,nf-console@1.0.4,nf-ga4gh@1.0.4,nf-google@1.4.5,nf-tower@1.5.6,nf-wave@0.5.4
Feb-23 11:52:27.883 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Feb-23 11:52:27.884 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Feb-23 11:52:27.888 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Feb-23 11:52:27.899 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Feb-23 11:52:27.916 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/ffeltus/.nextflow/scm
Feb-23 11:52:29.121 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/.git/config; branch: master; remote: origin; url: https://github.com/SystemsGenetics/GEMmaker.git
Feb-23 11:52:29.144 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Feb-23 11:52:29.155 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/.git/config; branch: master; remote: origin; url: https://github.com/SystemsGenetics/GEMmaker.git
Feb-23 11:52:29.925 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/nextflow.config
Feb-23 11:52:29.926 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/nextflow.config
Feb-23 11:52:29.939 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Feb-23 11:52:30.606 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, genotoul, alice, mjolnir_globe, uppmax, abims, nihbiowulf, nu_genomics, oist, sahmri, mpcdf, leicester, lugh, vsc_ugent, sage, cambridge, unibe_ibu, vai, podman, czbiohub_aws, jax, cheaha, ccga_med, test, scw, tigem, google, computerome, seg_globe, sanger, dkfz, pasteur, test_noclean, test_full, eddie, medair, azurebatch, bi, hki, bigpurple, sbc_sharc, adcra, crukmi, cedars, docker, engaging, gis, psmn, eva, ucl_myriad, utd_ganymede, charliecloud, fgcz, conda, crg, singularity, icr_davros, ceres, munin, rosalind, prince, hasta, hebbe, cfc, utd_sysbio, uzh, debug, genouest, cbe, ebc, ku_sund_dangpu, ccga_dx, crick, marvin, phoenix, biohpc_gen, shifter, mana, wehi, awsbatch, uct_hpc, imperial, maestro, aws_tower, binac]
Feb-23 11:52:30.654 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Feb-23 11:52:30.654 [main] INFO  nextflow.cli.CmdRun - Launching `https://github.com/systemsgenetics/gemmaker` [berserk_volta] DSL2 - revision: c7fe33612e [master]
Feb-23 11:52:30.655 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Feb-23 11:52:30.655 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Feb-23 11:52:30.658 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/ffeltus/.nextflow/secrets/store.json
Feb-23 11:52:30.662 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@191ec193] - activable => nextflow.secret.LocalSecretsProvider@191ec193
Feb-23 11:52:30.761 [main] DEBUG nextflow.Session - Session UUID: f96561b7-45cd-4bb4-9dc7-3940d2332054
Feb-23 11:52:30.761 [main] DEBUG nextflow.Session - Run name: berserk_volta
Feb-23 11:52:30.761 [main] DEBUG nextflow.Session - Executor pool size: 4
Feb-23 11:52:30.774 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=12; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Feb-23 11:52:30.805 [main] DEBUG nextflow.cli.CmdRun -
  Version: 22.10.7 build 5853
  Created: 18-02-2023 20:32 UTC (15:32 EDT)
  System: Linux 4.18.0-372.13.1.el8_6.x86_64
  Runtime: Groovy 3.0.13 on OpenJDK 64-Bit Server VM 11.0.15+10
  Encoding: UTF-8 (UTF-8)
  Process: 227723@node0578.palmetto.clemson.edu [10.125.3.68]
  CPUs: 4 - Mem: 128 GB (127.4 GB) - Swap: 2 GB (2 GB)
Feb-23 11:52:30.826 [main] DEBUG nextflow.Session - Work-dir: /home/ffeltus/athtest/work [nfs]
Feb-23 11:52:30.847 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Feb-23 11:52:30.859 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Feb-23 11:52:30.993 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Feb-23 11:52:31.008 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 5; maxThreads: 1000
Feb-23 11:52:31.158 [main] DEBUG nextflow.Session - Session start
Feb-23 11:52:31.164 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/ffeltus/athtest/results/pipeline_info/execution_trace_2023-02-23_11-52-30.txt
Feb-23 11:52:31.190 [main] DEBUG nextflow.Session - Using default localLib path: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/lib
Feb-23 11:52:31.195 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/lib
Feb-23 11:52:31.195 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/lib/nfcore_external_java_deps.jar
Feb-23 11:52:32.281 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Feb-23 11:52:32.461 [main] INFO  nextflow.Nextflow -

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  systemsgenetics/gemmaker v2.1.1
------------------------------------------------------
Core Nextflow options
  revision                  : master
  runName                   : berserk_volta
  containerEngine           : singularity
  launchDir                 : /home/ffeltus/athtest
  workDir                   : /home/ffeltus/athtest/work
  projectDir                : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker
  userName                  : ffeltus
  profile                   : singularity
  configFiles               : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/nextflow.config

Input/output options
  sras                      : SRAs.txt
  failed_run_report_template: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/failed_sra_runs.template.html
  multiqc_config_file       : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/multiqc_config.yaml
  multiqc_custom_logo       : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/systemsgenetics-gemmaker_logo.png

Kallisto Pipeline
  kallisto_index_path       : Arabidopsis_thaliana.TAIR10.cdna.all.fa.indexed
  kallisto_bootstrap_samples: 0

Reference genome options
  igenomes_ignore           : true

Generic options
  publish_dir_mode          : link

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use systemsgenetics/gemmaker for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.3620945

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/systemsgenetics/gemmaker/blob/master/CITATIONS.md
------------------------------------------------------
Feb-23 11:52:37.425 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-23 11:52:37.425 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.433 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Feb-23 11:52:37.439 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=4; memory=128 GB; capacity=4; pollInterval=100ms; dumpInterval=5m
Feb-23 11:52:37.520 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:retrieve_sra_metadata` matches process GEMmaker:retrieve_sra_metadata
Feb-23 11:52:37.522 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-23 11:52:37.522 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.561 [main] DEBUG nextflow.file.DirWatcherV2 - Watch service for path=/home/ffeltus/athtest/work/GEMmaker/process/; syntax=glob; pattern=*; skipHidden=true; events=create
Feb-23 11:52:37.600 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-23 11:52:37.600 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.610 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-23 11:52:37.610 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.617 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-23 11:52:37.617 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.629 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-23 11:52:37.629 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.639 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-23 11:52:37.639 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.647 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-23 11:52:37.647 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.658 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:local` matches labels `local` for process with name GEMmaker:next_sample
Feb-23 11:52:37.659 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Feb-23 11:52:37.659 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.681 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-23 11:52:37.681 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.689 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-23 11:52:37.689 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.699 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-23 11:52:37.700 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.721 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:local` matches labels `local` for process with name GEMmaker:clean_work_files
Feb-23 11:52:37.721 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Feb-23 11:52:37.721 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.724 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:local` matches labels `local` for process with name GEMmaker:clean_work_dirs
Feb-23 11:52:37.726 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Feb-23 11:52:37.726 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-23 11:52:37.729 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: GEMmaker:retrieve_sra_metadata, GEMmaker:multiqc, trimmomatic, samtools_sort, samtools_merge, clean_work_dirs, GEMmaker:kallisto_tpm, GEMmaker:failed_run_report, GEMmaker:kallisto, GEMmaker:next_sample, failed_run_report, get_software_versions, multiqc, GEMmaker:fastq_dump, GEMmaker:clean_work_dirs, star, next_sample, GEMmaker:clean_work_files, stringtie, stringtie_fpkm_tpm, retrieve_sra_metadata, salmon, fastqc_2, kallisto_tpm, fastqc_1, fastq_merge, GEMmaker:get_software_versions, create_gem, GEMmaker:download_runs, GEMmaker:create_gem, GET_SOFTWARE_VERSIONS, clean_work_files, kallisto, fastqc, GEMmaker:fastq_merge, fastq_dump, salmon_tpm, hisat2, download_runs, GEMmaker:fastqc_1, samtools_index
Feb-23 11:52:37.740 [main] DEBUG nextflow.Session - Igniting dataflow network (30)
Feb-23 11:52:37.741 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:get_software_versions
Feb-23 11:52:37.743 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:retrieve_sra_metadata
Feb-23 11:52:37.752 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:download_runs
Feb-23 11:52:37.753 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:fastq_dump
Feb-23 11:52:37.753 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:fastq_merge
Feb-23 11:52:37.754 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:fastqc_1
Feb-23 11:52:37.763 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:kallisto
Feb-23 11:52:37.763 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:kallisto_tpm
Feb-23 11:52:37.772 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:next_sample
Feb-23 11:52:37.773 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:multiqc
Feb-23 11:52:37.780 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:create_gem
Feb-23 11:52:37.781 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:failed_run_report
Feb-23 11:52:37.789 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:clean_work_files
Feb-23 11:52:37.789 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GEMmaker:clean_work_dirs
Feb-23 11:52:37.790 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Feb-23 11:52:37.790 [main] DEBUG nextflow.Session - Session await
Feb-23 11:52:37.858 [Actor Thread 1] WARN  nextflow.container.SingularityCache - Singularity cache directory has not been defined -- Remote image will be stored in the path: /home/ffeltus/athtest/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
Feb-23 11:52:37.860 [Actor Thread 1] INFO  nextflow.container.SingularityCache - Pulling Singularity image docker://systemsgenetics/gemmaker:2.1.0 [cache /home/ffeltus/athtest/work/singularity/systemsgenetics-gemmaker-2.1.0.img]
Feb-23 11:52:40.635 [Actor Thread 1] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=docker://systemsgenetics/gemmaker:2.1.0 path=/home/ffeltus/athtest/work/singularity/systemsgenetics-gemmaker-2.1.0.img
Feb-23 11:52:40.685 [Actor Thread 13] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/bin/retrieve_sra_metadata.py
Feb-23 11:52:40.768 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-23 11:52:40.834 [Task submitter] INFO  nextflow.Session - [40/3d215c] Submitted process > GEMmaker:retrieve_sra_metadata
Feb-23 11:52:44.220 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: GEMmaker:retrieve_sra_metadata; status: COMPLETED; exit: 0; error: -; workDir: /home/ffeltus/athtest/work/40/3d215c37850c911209e624c4c43ced]
Feb-23 11:52:44.831 [Actor Thread 13] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/bin/retrieve_sra_spots.py
Feb-23 11:52:44.832 [Actor Thread 13] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/bin/retrieve_sra.py
Feb-23 11:52:44.858 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-23 11:52:44.868 [Task submitter] INFO  nextflow.Session - [79/9a915a] Submitted process > GEMmaker:download_runs (SRX398816)
Feb-23 11:52:44.876 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-23 11:52:44.877 [Task submitter] INFO  nextflow.Session - [66/2db70b] Submitted process > GEMmaker:download_runs (SRX398817)
Feb-23 11:52:44.886 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-23 11:52:44.886 [Task submitter] INFO  nextflow.Session - [da/4663ac] Submitted process > GEMmaker:download_runs (SRX398814)
Feb-23 11:52:44.894 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-23 11:52:44.894 [Task submitter] INFO  nextflow.Session - [bc/e552c6] Submitted process > GEMmaker:download_runs (SRX398815)
Feb-23 11:52:47.780 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: GEMmaker:download_runs (SRX398816); status: COMPLETED; exit: 0; error: -; workDir: /home/ffeltus/athtest/work/79/9a915abd9eb7d667094e16e69c4ab6]
Feb-23 11:52:47.902 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process GEMmaker:download_runs > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Feb-23 11:52:47.917 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: GEMmaker:download_runs (SRX398814); status: COMPLETED; exit: 0; error: -; workDir: /home/ffeltus/athtest/work/da/4663ac26ba48a859fa89eb21ef90aa]
Feb-23 11:52:47.923 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process GEMmaker:download_runs > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Feb-23 11:52:47.942 [Task submitter] INFO  nextflow.Session - [3f/b59118] Submitted process > GEMmaker:next_sample (SRX398814)
Feb-23 11:52:47.951 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: GEMmaker:next_sample (SRX398814); status: COMPLETED; exit: -; error: -; workDir: /home/ffeltus/athtest/work/3f/b5911841498cc95fc738944acef6e8]
Feb-23 11:52:47.962 [Task submitter] INFO  nextflow.Session - [cb/003b3b] Submitted process > GEMmaker:next_sample (SRX398816)
Feb-23 11:52:47.970 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: GEMmaker:next_sample (SRX398816); status: COMPLETED; exit: -; error: -; workDir: /home/ffeltus/athtest/work/cb/003b3b278443e0fa237b329b427a61]
Feb-23 11:52:48.078 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: GEMmaker:download_runs (SRX398815); status: COMPLETED; exit: 0; error: -; workDir: /home/ffeltus/athtest/work/bc/e552c6c31657dfc58d6af1772492d1]
Feb-23 11:52:48.082 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process GEMmaker:download_runs > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Feb-23 11:52:48.091 [Task submitter] INFO  nextflow.Session - [01/e66cb5] Submitted process > GEMmaker:next_sample (SRX398815)
Feb-23 11:52:48.107 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: GEMmaker:next_sample (SRX398815); status: COMPLETED; exit: -; error: -; workDir: /home/ffeltus/athtest/work/01/e66cb5275c675c11e0408ec436890e]
Feb-23 11:52:48.230 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: GEMmaker:download_runs (SRX398817); status: COMPLETED; exit: 0; error: -; workDir: /home/ffeltus/athtest/work/66/2db70bcb9a236d1a541fc71a8e0baa]
Feb-23 11:52:48.234 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process GEMmaker:download_runs > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Feb-23 11:52:48.250 [Task submitter] INFO  nextflow.Session - [fa/1b1efa] Submitted process > GEMmaker:next_sample (SRX398817)
Feb-23 11:52:48.256 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: GEMmaker:next_sample (SRX398817); status: COMPLETED; exit: -; error: -; workDir: /home/ffeltus/athtest/work/fa/1b1efa9f020e656e88d7cbd4c6d576]
Feb-23 11:52:48.797 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-23 11:52:48.797 [Task submitter] INFO  nextflow.Session - [a1/540ea9] Submitted process > GEMmaker:download_runs (SRX398818)
Feb-23 11:52:48.804 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-23 11:52:48.804 [Task submitter] INFO  nextflow.Session - [21/51bc71] Submitted process > GEMmaker:download_runs (SRX398819)
Feb-23 11:52:48.846 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-23 11:52:48.846 [Task submitter] INFO  nextflow.Session - [26/b9feb2] Submitted process > GEMmaker:download_runs (SRX398821)
Feb-23 11:52:48.857 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-23 11:52:48.857 [Task submitter] INFO  nextflow.Session - [3e/bb9a5c] Submitted process > GEMmaker:download_runs (SRX398820)
Feb-23 11:52:52.212 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: GEMmaker:download_runs (SRX398818); status: COMPLETED; exit: 0; error: -; workDir: /home/ffeltus/athtest/work/a1/540ea93313008777fd61ce2ad8d8df]
Feb-23 11:52:52.217 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process GEMmaker:download_runs > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Feb-23 11:52:52.224 [Task submitter] INFO  nextflow.Session - [6a/9a841b] Submitted process > GEMmaker:next_sample (SRX398818)
Feb-23 11:52:52.229 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: GEMmaker:download_runs (SRX398819); status: COMPLETED; exit: 0; error: -; workDir: /home/ffeltus/athtest/work/21/51bc71e03bd3dddccfd1b2b6fb072c]
Feb-23 11:52:52.232 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process GEMmaker:download_runs > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Feb-23 11:52:52.238 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: GEMmaker:download_runs (SRX398821); status: COMPLETED; exit: 0; error: -; workDir: /home/ffeltus/athtest/work/26/b9feb2f619d8a078811aeeab2edf00]
Feb-23 11:52:52.243 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process GEMmaker:download_runs > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Feb-23 11:52:52.249 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: GEMmaker:download_runs (SRX398820); status: COMPLETED; exit: 0; error: -; workDir: /home/ffeltus/athtest/work/3e/bb9a5c90bd2a0859d35dfeae55e242]
Feb-23 11:52:52.253 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process GEMmaker:download_runs > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Feb-23 11:52:52.312 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: GEMmaker:next_sample (SRX398818); status: COMPLETED; exit: -; error: -; workDir: /home/ffeltus/athtest/work/6a/9a841b776663a6e7a1820749678b1f]
Feb-23 11:52:52.312 [Task submitter] INFO  nextflow.Session - [8e/6d556e] Submitted process > GEMmaker:next_sample (SRX398819)
Feb-23 11:52:52.317 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: GEMmaker:next_sample (SRX398819); status: COMPLETED; exit: -; error: -; workDir: /home/ffeltus/athtest/work/8e/6d556e2d858f01ce2454d815be27ea]
Feb-23 11:52:52.317 [Task submitter] INFO  nextflow.Session - [f4/e97c14] Submitted process > GEMmaker:next_sample (SRX398820)
Feb-23 11:52:52.322 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: GEMmaker:next_sample (SRX398820); status: COMPLETED; exit: -; error: -; workDir: /home/ffeltus/athtest/work/f4/e97c148fdef594165c47f4c68dcb49]
Feb-23 11:52:52.323 [Task submitter] INFO  nextflow.Session - [b4/2401bb] Submitted process > GEMmaker:next_sample (SRX398821)
Feb-23 11:52:52.422 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: GEMmaker:next_sample (SRX398821); status: COMPLETED; exit: -; error: -; workDir: /home/ffeltus/athtest/work/b4/2401bbc33287cce629b35061dd528b]
Feb-23 11:52:52.795 [Actor Thread 7] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/failed_sra_runs.template.html
Feb-23 11:52:52.795 [Actor Thread 7] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/bin/failed_runs_report.py
Feb-23 11:52:52.805 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-23 11:52:52.805 [Task submitter] INFO  nextflow.Session - [30/2cc3e0] Submitted process > GEMmaker:failed_run_report
Feb-23 11:52:53.624 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: GEMmaker:failed_run_report; status: COMPLETED; exit: 0; error: -; workDir: /home/ffeltus/athtest/work/30/2cc3e08f1349e946543e6a07a9986a]
Feb-23 11:52:53.627 [main] DEBUG nextflow.Session - Session await > all processes finished
Feb-23 11:52:53.630 [main] DEBUG nextflow.Session - Session await > all barriers passed
Feb-23 11:52:53.638 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=18; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=20.3s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=4; peakCpus=4; peakMemory=8 GB; ]
Feb-23 11:52:53.638 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Feb-23 11:52:53.640 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Feb-23 11:52:53.677 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  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(SRX398815)","maxLabel":"GEMmaker:download_runs (SRX398814)","q1Label":"GEMmaker:download_runs (SRX398817)","q2Label":"GEMmaker:download_runs (SRX398819)","q3Label":"GEMmaker:download_runs (SRX398820)"},"process":"download_runs","mem":{"mean":38818816,"min":26263552,"q1":32348160,"q2":37191680,"q3":45713408,"max":52191232,"minLabel":"GEMmaker:download_runs (SRX398815)","maxLabel":"GEMmaker:download_runs (SRX398814)","q1Label":"GEMmaker:download_runs (SRX398817)","q2Label":"GEMmaker:download_runs (SRX398816)","q3Label":"GEMmaker:download_runs (SRX398820)"},"memUsage":{"mean":1.81,"min":1.22,"q1":1.51,"q2":1.73,"q3":2.13,"max":2.43,"minLabel":"GEMmaker:download_runs (SRX398815)","maxLabel":"GEMmaker:download_runs (SRX398814)","q1Label":"GEMmaker:download_runs (SRX398817)","q2Label":"GEMmaker:download_runs (SRX398816)","q3Label":"GEMmaker:download_runs (SRX398820)"},"timeUsage":null,"vmem":{"mean":473932800,"min":470200320,"q1":471982080,"q2":472924160,"q3":473997312,"max":483454976,"minLabel":"GEMmaker:download_runs (SRX398816)","maxLabel":"GEMmaker:download_runs (SRX398819)","q1Label":"GEMmaker:download_runs (SRX398817)","q2Label":"GEMmaker:download_runs (SRX398815)","q3Label":"GEMmaker:download_runs (SRX398814)"},"reads":{"mean":15444574.75,"min":15444569,"q1":15444571.25,"q2":15444575.5,"q3":15444578.25,"max":15444580,"minLabel":"GEMmaker:download_runs (SRX398818)","maxLabel":"GEMmaker:download_runs (SRX398815)","q1Label":"GEMmaker:download_runs (SRX398821)","q2Label":"GEMmaker:download_runs (SRX398820)","q3Label":"GEMmaker:download_runs (SRX398814)"},"cpu":{"mean":46.49,"min":43.5,"q1":44.28,"q2":47.2,"q3":47.83,"max":49.8,"minLabel":"GEMmaker:download_runs (SRX398815)","maxLabel":"GEMmaker:download_runs (SRX398814)","q1Label":"GEMmaker:download_runs (SRX398817)","q2Label":"GEMmaker:download_runs (SRX398819)","q3Label":"GEMmaker:download_runs (SRX398820)"},"time":{"mean":2248.25,"min":2156,"q1":2201,"q2":2218,"q3":2260,"max":2424,"minLabel":"GEMmaker:download_runs (SRX398819)","maxLabel":"GEMmaker:download_runs (SRX398817)","q1Label":"GEMmaker:download_runs (SRX398816)","q2Label":"GEMmaker:download_runs (SRX398814)","q3Label":"GEMmaker:download_runs (SRX398820)"},"writes":{"mean":5141.88,"min":5141,"q1":5142,"q2":5142,"q3":5142,"max":5142,"minLabel":"GEMmaker:download_runs (SRX398821)","maxLabel":"GEMmaker:download_runs (SRX398820)","q1Label":"GEMmaker:download_runs (SRX398816)","q2Label":"GEMmaker:download_runs (SRX398815)","q3Label":"GEMmaker:download_runs (SRX398818)"}},{"cpuUsage":null,"process":"next_sample","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":1.25,"min":0,"q1":1,"q2":1,"q3":1.25,"max":3,"minLabel":"GEMmaker:next_sample (SRX398817)","maxLabel":"GEMmaker:next_sample (SRX398814)","q1Label":"GEMmaker:next_sample (SRX398815)","q2Label":"GEMmaker:next_sample (SRX398819)","q3Label":"GEMmaker:next_sample (SRX398821)"},"writes":null},{"cpuUsage":{"mean":45.6,"min":45.6,"q1":45.6,"q2":45.6,"q3":45.6,"max":45.6,"minLabel":"GEMmaker:failed_run_report","maxLabel":"GEMmaker:failed_run_report","q1Label":"GEMmaker:failed_run_report","q2Label":"GEMmaker:failed_run_report","q3Label":"GEMmaker:failed_run_report"},"process":"failed_run_report","mem":{"mean":10375168,"min":10375168,"q1":10375168,"q2":10375168,"q3":10375168,"max":10375168,"minLabel":"GEMmaker:failed_run_report","maxLabel":"GEMmaker:failed_run_report","q1Label":"GEMmaker:failed_run_report","q2Label":"GEMmaker:failed_run_report","q3Label":"GEMmaker:failed_run_report"},"memUsage":{"mean":0.48,"min":0.48,"q1":0.48,"q2":0.48,"q3":0.48,"max":0.48,"minLabel":"GEMmaker:failed_run_report","maxLabel":"GEMmaker:failed_run_report","q1Label":"GEMmaker:failed_run_report","q2Label":"GEMmaker:failed_run_report","q3Label":"GEMmaker:failed_run_report"},"timeUsage":null,"vmem":{"mean":16449536,"min":16449536,"q1":16449536,"q2":16449536,"q3":16449536,"max":16449536,"minLabel":"GEMmaker:failed_run_report","maxLabel":"GEMmaker:failed_run_report","q1Label":"GEMmaker:failed_run_report","q2Label":"GEMmaker:failed_run_report","q3Label":"GEMmaker:failed_run_report"},"reads":{"mean":2152430,"min":2152430,"q1":2152430,"q2":2152430,"q3":2152430,"max":2152430,"minLabel":"GEMmaker:failed_run_report","maxLabel":"GEMmaker:failed_run_report","q1Label":"GEMmaker:failed_run_report","q2Label":"GEMmaker:failed_run_report","q3Label":"GEMmaker:failed_run_report"},"cpu":{"mean":45.6,"min":45.6,"q1":45.6,"q2":45.6,"q3":45.6,"max":45.6,"minLabel":"GEMmaker:failed_run_report","maxLabel":"GEMmaker:failed_run_report","q1Label":"GEMmaker:failed_run_report","q2Label":"GEMmaker:failed_run_report","q3Label":"GEMmaker:failed_run_report"},"time":{"mean":289,"min":289,"q1":289,"q2":289,"q3":289,"max":289,"minLabel":"GEMmaker:failed_run_report","maxLabel":"GEMmaker:failed_run_report","q1Label":"GEMmaker:failed_run_report","q2Label":"GEMmaker:failed_run_report","q3Label":"GEMmaker:failed_run_report"},"writes":{"mean":3798,"min":3798,"q1":3798,"q2":3798,"q3":3798,"max":3798,"minLabel":"GEMmaker:failed_run_report","maxLabel":"GEMmaker:failed_run_report","q1Label":"GEMmaker:failed_run_report","q2Label":"GEMmaker:failed_run_report","q3Label":"GEMmaker:failed_run_report"}}]
Feb-23 11:52:54.331 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Feb-23 11:52:54.854 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Feb-23 11:52:54.879 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Feb-23 11:52:54.880 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

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@feltus feltus added the bug label Feb 23, 2023
@spficklin
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Sorry for the slow response. I can't seem to duplicate the problem. Are you still having the issue?

@feltus
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feltus commented Mar 8, 2023 via email

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@spficklin spficklin

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