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singularity: No such file or directory #234

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ropolomx opened this issue Sep 18, 2021 · 2 comments
Closed
4 tasks done

singularity: No such file or directory #234

ropolomx opened this issue Sep 18, 2021 · 2 comments
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@ropolomx
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ropolomx commented Sep 18, 2021 •
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Check Documentation

I have checked the following places for your error:

Description of the bug

Command:

nextflow run nf-core/mag -r 2.1.0 -profile test,singularity -c sge.conf

Error:

Error executing process > 'NFCORE_MAG:MAG:KRAKEN2_DB_PREPARATION'

Caused by:
  Process `NFCORE_MAG:MAG:KRAKEN2_DB_PREPARATION` terminated with an error exit status (127)

Command executed:

  mkdir db_tmp
  tar -xf "minigut_kraken.tgz" -C db_tmp
  mkdir database
  mv `find db_tmp/ -name "*.k2d"` database/

Command exit status:
  127

Command output:
  (empty)

Command error:
  env: singularity: No such file or directory

Work dir:
  /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/0e/c9cba40483c7e9397b2e23412fad15

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

sge.conf:

process {
    executor = 'sge'
    clusterOptions = '-cwd -V'
    penv = 'smp'
}

executor {
    submitRateLimit = '10 sec'
    queueSize = 10
}
singularity {
    enabled = true
    autoMounts = true
}

Steps to reproduce

Steps to reproduce the behaviour:

  1. Command line: as above
  2. See error: as above

Expected behaviour

Pipeline would launch jobs with the sge executor using Singularity images.

Log files

Have you provided the following extra information/files:

  • The command used to run the pipeline
  • The .nextflow.log file 
Sep-17 23:44:46.975 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/mag -r 2.1.0 -profile test,singularity -c sge.conf
Sep-17 23:44:47.189 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 21.04.0
Sep-17 23:44:48.835 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/AAFC-AAC/ortegapoloro/assets/nf-core/mag/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/mag.git
Sep-17 23:44:48.848 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/AAFC-AAC/ortegapoloro/assets/nf-core/mag/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/mag.git
Sep-17 23:44:50.602 [main] INFO  nextflow.cli.CmdRun - Launching `nf-core/mag` [angry_hugle] - revision: d4f00bc2d1 [2.1.0]
Sep-17 23:44:51.604 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/AAFC-AAC/ortegapoloro/assets/nf-core/mag/nextflow.config
Sep-17 23:44:51.612 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/sge.conf
Sep-17 23:44:51.612 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/AAFC-AAC/ortegapoloro/assets/nf-core/mag/nextflow.config
Sep-17 23:44:51.612 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/sge.conf
Sep-17 23:44:51.625 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,singularity`
Sep-17 23:44:52.395 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Sep-17 23:44:52.397 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Sep-17 23:44:52.400 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Sep-17 23:44:53.244 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,singularity`
Sep-17 23:44:53.292 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, genotoul, uppmax, abims, nu_genomics, imperial_mb, oist, mpcdf, lugh, cambridge, podman, czbiohub_aws, jax, ccga_med, test, google, computerome, seg_globe, sanger, pasteur, test_full, eddie, test_host_rm, bi, bigpurple, docker, gis, eva, utd_ganymede, charliecloud, conda, singularity, icr_davros, munin, rosalind, prince, hebbe, cfc, utd_sysbio, uzh, test_hybrid_host_rm, debug, test_busco_auto, genouest, cbe, ebc, ccga_dx, test_hybrid, crick, phoenix, biohpc_gen, shifter, awsbatch, uct_hpc, imperial, aws_tower, binac]
Sep-17 23:44:53.311 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/AAFC-AAC/ortegapoloro/plugins
Sep-17 23:44:53.313 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Sep-17 23:44:53.340 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins local root: .nextflow/plr/21921f6807262d1f701978cdf8a1f5c4
Sep-17 23:44:53.346 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Sep-17 23:44:53.346 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Sep-17 23:44:53.348 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Sep-17 23:44:53.382 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.1.0' resolved
Sep-17 23:44:53.395 [main] DEBUG nextflow.plugin.PluginUpdater - Starting plugin nf-tower version: 1.1.0
Sep-17 23:44:53.396 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.1.0'
Sep-17 23:44:53.409 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.1.0
Sep-17 23:44:53.496 [main] DEBUG nextflow.Session - Session uuid: 97698a1e-c5e2-478d-a4ad-9e6e0119c421
Sep-17 23:44:53.496 [main] DEBUG nextflow.Session - Run name: angry_hugle
Sep-17 23:44:53.497 [main] DEBUG nextflow.Session - Executor pool size: 80
Sep-17 23:44:53.512 [main] DEBUG nextflow.cli.CmdRun -
  Version: 21.04.0 build 5552
  Created: 02-05-2021 16:22 UTC (12:22 EDT)
  System: Linux 3.10.0-957.21.3.el7.x86_64
  Runtime: Groovy 3.0.7 on OpenJDK 64-Bit Server VM 1.8.0_212-b04
  Encoding: UTF-8 (UTF-8)
  Process: 80334@biocluster.agr.gc.ca [10.128.144.240]
  CPUs: 80 - Mem: 1007.6 GB (2.9 GB) - Swap: 4 GB (3.2 GB)
Sep-17 23:44:53.546 [main] DEBUG nextflow.Session - Work-dir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work [nfs]
Sep-17 23:44:53.575 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Sep-17 23:44:53.592 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Sep-17 23:44:53.616 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Sep-17 23:44:53.918 [main] DEBUG nextflow.Session - Session start invoked
Sep-17 23:44:53.924 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/results/pipeline_info/execution_trace_2021-09-17_23-44-53.txt
Sep-17 23:44:53.958 [main] DEBUG nextflow.Session - Using default localLib path: /home/AAFC-AAC/ortegapoloro/assets/nf-core/mag/lib
Sep-17 23:44:53.965 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/AAFC-AAC/ortegapoloro/assets/nf-core/mag/lib
Sep-17 23:44:53.965 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/AAFC-AAC/ortegapoloro/assets/nf-core/mag/lib/nfcore_external_java_deps.jar
Sep-17 23:44:54.980 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Sep-17 23:44:55.283 [main] INFO  nextflow.Nextflow -

-ESC[2m----------------------------------------------------ESC[0m-
                                        ESC[0;32m,--.ESC[0;30m/ESC[0;32m,-.ESC[0m
ESC[0;34m        ___     __   __   __   ___     ESC[0;32m/,-._.--~'ESC[0m
ESC[0;34m  |\ | |__  __ /  ` /  \ |__) |__         ESC[0;33m}  {ESC[0m
ESC[0;34m  | \| |       \__, \__/ |  \ |___     ESC[0;32m\`-._,-`-,ESC[0m
                                        ESC[0;32m`._,._,'ESC[0m
ESC[0;35m  nf-core/mag v2.1.0ESC[0m
-ESC[2m----------------------------------------------------ESC[0m-
ESC[1mCore Nextflow optionsESC[0m
  ESC[0;34mrevision                   : ESC[0;32m2.1.0ESC[0m
  ESC[0;34mrunName                    : ESC[0;32mangry_hugleESC[0m
  ESC[0;34mcontainerEngine            : ESC[0;32msingularityESC[0m
  ESC[0;34mlaunchDir                  : ESC[0;32m/isilon/lethbridge-rdc/users/ortegapoloro/mag_testESC[0m
  ESC[0;34mworkDir                    : ESC[0;32m/isilon/lethbridge-rdc/users/ortegapoloro/mag_test/workESC[0m
  ESC[0;34mprojectDir                 : ESC[0;32m/home/AAFC-AAC/ortegapoloro/assets/nf-core/magESC[0m
  ESC[0;34muserName                   : ESC[0;32mortegapoloroESC[0m
  ESC[0;34mprofile                    : ESC[0;32mtest,singularityESC[0m
  ESC[0;34mconfigFiles                : ESC[0;32m/home/AAFC-AAC/ortegapoloro/assets/nf-core/mag/nextflow.config, /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/sge.confESC[0m

ESC[1mInput/output optionsESC[0m
  ESC[0;34minput                      : ESC[0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.csvESC[0m

ESC[1mInstitutional config optionsESC[0m
  ESC[0;34mconfig_profile_name        : ESC[0;32mTest profileESC[0m
  ESC[0;34mconfig_profile_description : ESC[0;32mMinimal test dataset to check pipeline functionESC[0m

ESC[1mMax job request optionsESC[0m
  ESC[0;34mmax_cpus                   : ESC[0;32m2ESC[0m
  ESC[0;34mmax_memory                 : ESC[0;32m6 GBESC[0m
  ESC[0;34mmax_time                   : ESC[0;32m6hESC[0m

ESC[1mQuality control for short reads optionsESC[0m
  ESC[0;34mphix_reference             : ESC[0;32m/home/AAFC-AAC/ortegapoloro/assets/nf-core/mag/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gzESC[0m

ESC[1mQuality control for long reads optionsESC[0m
  ESC[0;34mlambda_reference           : ESC[0;32m/home/AAFC-AAC/ortegapoloro/assets/nf-core/mag/assets/data/GCA_000840245.1_ViralProj14204_genomic.fna.gzESC[0m

ESC[1mTaxonomic profiling optionsESC[0m
  ESC[0;34mcentrifuge_db              : ESC[0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_cf.tar.gzESC[0m
  ESC[0;34mkraken2_db                 : ESC[0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_kraken.tgzESC[0m
  ESC[0;34mskip_krona                 : ESC[0;32mtrueESC[0m
  ESC[0;34mgtdb                       : ESC[0;32mfalseESC[0m

ESC[1mBinning optionsESC[0m
  ESC[0;34mmin_length_unbinned_contigs: ESC[0;32m1ESC[0m
  ESC[0;34mmax_unbinned_contigs       : ESC[0;32m2ESC[0m
ESC[1mBin quality check optionsESC[0m
  ESC[0;34mbusco_reference            : ESC[0;32mhttps://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gzESC[0m

!! Only displaying parameters that differ from the pipeline defaults !!
-ESC[2m----------------------------------------------------ESC[0m-
If you use nf-core/mag for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.3589527

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

* Software dependencies
  https://github.com/nf-core/mag/blob/master/CITATIONS.md
-ESC[2m----------------------------------------------------ESC[0m-
Sep-17 23:45:06.769 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: MAG_DEPTHS_PLOT, NANOPLOT_FILTERED, BUSCO, BOWTIE2_ASSEMBLY_BUILD, FASTP, BOWTIE2_PHIX_REMOVAL_ALIGN, BUSCO_DB_PREPARATION, BOWTIE2_HOST_REMOVAL_ALIGN, POOL_SINGLE_READS, CENTRIFUGE_DB_PREPARATION, FASTQC_TRIMMED, FASTQC_RAW, BOWTIE2_ASSEMBLY_ALIGN, QUAST, QUAST_BINS_SUMMARY, CENTRIFUGE, KRAKEN2_DB_PREPARATION, POOL_PAIRED_READS, BOWTIE2_REMOVAL_ALIGN, BUSCO_SAVE_DOWNLOAD, FILTLONG, KRAKEN2, METABAT2, GET_SOFTWARE_VERSIONS, KRONA_DB, CAT_DB, CAT, PORECHOP, NANOPLOT, KRONA, FASTQC, MEGAHIT, CAT_DB_GENERATE, MAG_DEPTHS_SUMMARY, BOWTIE2_HOST_REMOVAL_BUILD, SPADES, GTDBTK_SUMMARY, MULTIQC, MAG_DEPTHS, BIN_SUMMARY, BOWTIE2_REMOVAL_BUILD, POOL_LONG_READS, QUAST_BINS, GTDBTK_CLASSIFY, NANOPLOT_RAW, GTDBTK_DB_PREPARATION, BOWTIE2_PHIX_REMOVAL_BUILD, BUSCO_PLOT, BUSCO_SUMMARY, NANOLYSE, SPADESHYBRID
Sep-17 23:45:06.876 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_MAG:MAG:FASTQC_RAW
Sep-17 23:45:06.883 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:06.883 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:06.892 [main] DEBUG nextflow.executor.Executor - [warm up] executor > sge
Sep-17 23:45:06.898 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'sge' > capacity: 10; pollInterval: 5s; dumpInterval: 5m
Sep-17 23:45:06.901 [main] DEBUG n.processor.TaskPollingMonitor - Creating submit rate limit of 10 reqs by 1 seconds
Sep-17 23:45:06.905 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'sge' > queue-stat-interval: 1m
Sep-17 23:45:06.987 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_MAG:MAG:FASTP
Sep-17 23:45:06.990 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:06.990 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.001 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.001 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.007 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BOWTIE2_PHIX_REMOVAL_ALIGN` matches process NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_ALIGN
Sep-17 23:45:07.008 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.008 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.016 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_MAG:MAG:FASTQC_TRIMMED
Sep-17 23:45:07.017 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.017 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.024 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.024 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.032 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PORECHOP` matches process NFCORE_MAG:MAG:PORECHOP
Sep-17 23:45:07.033 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.033 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.042 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NANOLYSE` matches process NFCORE_MAG:MAG:NANOLYSE
Sep-17 23:45:07.043 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.043 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.063 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FILTLONG` matches process NFCORE_MAG:MAG:FILTLONG
Sep-17 23:45:07.064 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.064 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.064 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.072 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.073 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.077 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.077 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.084 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CENTRIFUGE` matches process NFCORE_MAG:MAG:CENTRIFUGE
Sep-17 23:45:07.085 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.085 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.093 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.093 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.099 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KRAKEN2` matches process NFCORE_MAG:MAG:KRAKEN2
Sep-17 23:45:07.100 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.100 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.112 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MEGAHIT` matches process NFCORE_MAG:MAG:MEGAHIT
Sep-17 23:45:07.112 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.112 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.125 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SPADES` matches process NFCORE_MAG:MAG:SPADES
Sep-17 23:45:07.127 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.127 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.155 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SPADESHYBRID` matches process NFCORE_MAG:MAG:SPADESHYBRID
Sep-17 23:45:07.156 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.156 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.167 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.167 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.174 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.175 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.186 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BOWTIE2_ASSEMBLY_ALIGN` matches process NFCORE_MAG:MAG:METABAT2_BINNING:BOWTIE2_ASSEMBLY_ALIGN
Sep-17 23:45:07.187 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.187 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.198 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:METABAT2` matches process NFCORE_MAG:MAG:METABAT2_BINNING:METABAT2
Sep-17 23:45:07.199 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.199 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.205 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MAG_DEPTHS` matches process NFCORE_MAG:MAG:METABAT2_BINNING:MAG_DEPTHS
Sep-17 23:45:07.206 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.206 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.241 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.241 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.245 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.245 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.258 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.258 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.272 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BUSCO` matches process NFCORE_MAG:MAG:BUSCO_QC:BUSCO
Sep-17 23:45:07.273 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.273 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.281 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.281 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.290 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.290 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.299 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.299 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.305 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.310 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT` matches process NFCORE_MAG:MAG:CAT
Sep-17 23:45:07.311 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.311 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.319 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.319 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.329 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.329 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.352 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_MAG:MAG:MULTIQC
Sep-17 23:45:07.352 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: sge
Sep-17 23:45:07.352 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'sge'
Sep-17 23:45:07.359 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Sep-17 23:45:07.360 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Sep-17 23:45:07.360 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Sep-17 23:45:07.360 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Sep-17 23:45:07.360 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Sep-17 23:45:07.360 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Sep-17 23:45:07.360 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Sep-17 23:45:07.361 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Sep-17 23:45:07.361 [main] DEBUG nextflow.Session - Ignite dataflow network (59)
Sep-17 23:45:07.362 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:FASTQC_RAW
Sep-17 23:45:07.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:FASTP
Sep-17 23:45:07.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_BUILD
Sep-17 23:45:07.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_ALIGN
Sep-17 23:45:07.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:FASTQC_TRIMMED
Sep-17 23:45:07.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:NANOPLOT_RAW
Sep-17 23:45:07.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:PORECHOP
Sep-17 23:45:07.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:NANOLYSE
Sep-17 23:45:07.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:FILTLONG
Sep-17 23:45:07.366 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:NANOPLOT_FILTERED
Sep-17 23:45:07.367 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:CENTRIFUGE_DB_PREPARATION
Sep-17 23:45:07.368 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:CENTRIFUGE
Sep-17 23:45:07.368 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:KRAKEN2_DB_PREPARATION
Sep-17 23:45:07.368 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:KRAKEN2
Sep-17 23:45:07.368 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:MEGAHIT
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:SPADES
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:SPADESHYBRID
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:QUAST
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:METABAT2_BINNING:BOWTIE2_ASSEMBLY_BUILD
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:METABAT2_BINNING:BOWTIE2_ASSEMBLY_ALIGN
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:METABAT2_BINNING:METABAT2
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:METABAT2_BINNING:MAG_DEPTHS
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:METABAT2_BINNING:MAG_DEPTHS_PLOT
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:METABAT2_BINNING:MAG_DEPTHS_SUMMARY
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:BUSCO_QC:BUSCO_DB_PREPARATION
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:BUSCO_QC:BUSCO
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:BUSCO_QC:BUSCO_PLOT
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:BUSCO_QC:BUSCO_SUMMARY
Sep-17 23:45:07.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:QUAST_BINS
Sep-17 23:45:07.370 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:QUAST_BINS_SUMMARY
Sep-17 23:45:07.370 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:CAT
Sep-17 23:45:07.370 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:BIN_SUMMARY
Sep-17 23:45:07.370 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:GET_SOFTWARE_VERSIONS
Sep-17 23:45:07.371 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAG:MAG:MULTIQC
Sep-17 23:45:07.374 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Sep-17 23:45:07.374 [main] DEBUG nextflow.Session - Session await
Sep-17 23:45:08.055 [Actor Thread 6] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1; path=/isilon/lethbridge-rdc/users/ortegapoloro/singularity_cache/depot.galaxyproject.org-singularity-bowtie2-2.4.2--py38h1c8e9b9_1.img
Sep-17 23:45:08.074 [Actor Thread 16] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/AAFC-AAC/ortegapoloro/assets/nf-core/mag/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz
Sep-17 23:45:08.104 [Actor Thread 10] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.021 s; total time: 0.022 s
Sep-17 23:45:08.115 [Actor Thread 10] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /scratch/8aa3f41aab3e922a0b88d341517a0103.collect-file
Sep-17 23:45:08.126 [Actor Thread 10] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /scratch/nxf-4870470095605463834
Sep-17 23:45:08.134 [Actor Thread 12] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=240; maxQueueSize=720; keepAlive=1m
Sep-17 23:45:08.144 [FileTransfer-thread-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_kraken.tgz at /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/stage/72/d3070105e220b14eac7b9ec53d9a5c/minigut_kraken.tgz
Sep-17 23:45:08.174 [FileTransfer-thread-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_cf.tar.gz at /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/stage/b7/b08abd15193252d1bd8b3387d94cd2/minigut_cf.tar.gz
Sep-17 23:45:08.174 [Actor Thread 10] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img; path=/isilon/lethbridge-rdc/users/ortegapoloro/singularity_cache/containers.biocontainers.pro-s3-SingImgsRepo-biocontainers-v1.2.0_cv1-biocontainers_v1.2.0_cv1.img.img
Sep-17 23:45:09.189 [FileTransfer-thread-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz at /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/stage/c9/367883f6bcdca36f983f9ad75a0112/bacteria_odb10.2020-03-06.tar.gz
Sep-17 23:45:11.896 [FileTransfer-thread-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz at /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/stage/ca/f923e98d13d92ad3e6fd2fdd5a964e/test_minigut_R1.fastq.gz
Sep-17 23:45:11.913 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SGE] submitted process NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_BUILD (GCA_002596845.1_ASM259684v1_genomic.fna.gz) > jobId: 1546693; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/a6/c6e62b1cb7526f3f26c1804af45b0d
Sep-17 23:45:11.922 [Task submitter] INFO  nextflow.Session - [a6/c6e62b] Submitted process > NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_BUILD (GCA_002596845.1_ASM259684v1_genomic.fna.gz)
Sep-17 23:45:12.489 [FileTransfer-thread-5] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R2.fastq.gz at /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/stage/dc/7212d436fe995492d4a6ca27bfd882/test_minigut_R2.fastq.gz
Sep-17 23:45:13.083 [FileTransfer-thread-6] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz at /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/stage/ca/f923e98d13d92ad3e6fd2fdd5a964e/test_minigut_R1.fastq.gz
Sep-17 23:45:13.683 [FileTransfer-thread-7] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R1.fastq.gz at /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/stage/57/815e839cad2b233611c21d7d0dac54/test_minigut_sample2_R1.fastq.gz
Sep-17 23:45:14.279 [FileTransfer-thread-8] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R2.fastq.gz at /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/stage/8c/3dcfafb9bc4a7a285231effb885407/test_minigut_sample2_R2.fastq.gz
Sep-17 23:45:14.865 [FileTransfer-thread-9] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R1.fastq.gz at /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/stage/57/815e839cad2b233611c21d7d0dac54/test_minigut_sample2_R1.fastq.gz
Sep-17 23:45:14.874 [Actor Thread 16] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0; path=/isilon/lethbridge-rdc/users/ortegapoloro/singularity_cache/depot.galaxyproject.org-singularity-fastqc-0.11.9--0.img
Sep-17 23:45:14.874 [Actor Thread 13] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/fastp:0.20.1--h8b12597_0; path=/isilon/lethbridge-rdc/users/ortegapoloro/singularity_cache/depot.galaxyproject.org-singularity-fastp-0.20.1--h8b12597_0.img
Sep-17 23:45:15.756 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SGE] submitted process NFCORE_MAG:MAG:KRAKEN2_DB_PREPARATION > jobId: 1546694; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/0e/c9cba40483c7e9397b2e23412fad15
Sep-17 23:45:15.756 [Task submitter] INFO  nextflow.Session - [0e/c9cba4] Submitted process > NFCORE_MAG:MAG:KRAKEN2_DB_PREPARATION
Sep-17 23:45:19.767 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SGE] submitted process NFCORE_MAG:MAG:CENTRIFUGE_DB_PREPARATION > jobId: 1546695; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/b5/591599b985a2b2ed5f7ebe82c57a58
Sep-17 23:45:19.768 [Task submitter] INFO  nextflow.Session - [b5/591599] Submitted process > NFCORE_MAG:MAG:CENTRIFUGE_DB_PREPARATION
Sep-17 23:45:23.637 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SGE] submitted process NFCORE_MAG:MAG:BUSCO_QC:BUSCO_DB_PREPARATION (bacteria_odb10.2020-03-06.tar) > jobId: 1546696; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/a7/e3616a3006eaef52a57651b1b5b6be
Sep-17 23:45:23.639 [Task submitter] INFO  nextflow.Session - [a7/e3616a] Submitted process > NFCORE_MAG:MAG:BUSCO_QC:BUSCO_DB_PREPARATION (bacteria_odb10.2020-03-06.tar)
Sep-17 23:45:27.457 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SGE] submitted process NFCORE_MAG:MAG:FASTQC_RAW (test_minigut) > jobId: 1546697; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/fe/fb4ac7d70622167bbdf5d80c3b7632
Sep-17 23:45:27.458 [Task submitter] INFO  nextflow.Session - [fe/fb4ac7] Submitted process > NFCORE_MAG:MAG:FASTQC_RAW (test_minigut)
Sep-17 23:45:31.088 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SGE] submitted process NFCORE_MAG:MAG:FASTQC_RAW (test_minigut_sample2) > jobId: 1546698; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/42/1315abd9abfc459b43e7162e5fd10f
Sep-17 23:45:31.089 [Task submitter] INFO  nextflow.Session - [42/1315ab] Submitted process > NFCORE_MAG:MAG:FASTQC_RAW (test_minigut_sample2)
Sep-17 23:45:34.739 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SGE] submitted process NFCORE_MAG:MAG:FASTP (test_minigut_sample2) > jobId: 1546699; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/a0/ffd7f07923067fa760de2df6177b0c
Sep-17 23:45:34.740 [Task submitter] INFO  nextflow.Session - [a0/ffd7f0] Submitted process > NFCORE_MAG:MAG:FASTP (test_minigut_sample2)
Sep-17 23:45:38.634 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SGE] submitted process NFCORE_MAG:MAG:FASTP (test_minigut) > jobId: 1546700; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/81/c3235984061abad0d5c5782ce88274
Sep-17 23:45:38.635 [Task submitter] INFO  nextflow.Session - [81/c32359] Submitted process > NFCORE_MAG:MAG:FASTP (test_minigut)
Sep-17 23:45:51.944 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1546694; id: 2; name: NFCORE_MAG:MAG:KRAKEN2_DB_PREPARATION; status: COMPLETED; exit: 127; error: -; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/0e/c9cba40483c7e9397b2e23412fad15 started: 1631936751923; exited: 2021-09-18T03:45:50.009187Z; ]
Sep-17 23:45:51.987 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_MAG:MAG:KRAKEN2_DB_PREPARATION'

Caused by:
  Process `NFCORE_MAG:MAG:KRAKEN2_DB_PREPARATION` terminated with an error exit status (127)

Command executed:

  mkdir db_tmp
  tar -xf "minigut_kraken.tgz" -C db_tmp
  mkdir database
  mv `find db_tmp/ -name "*.k2d"` database/

Command exit status:
  127

Command output:
  (empty)

Command error:
  env: singularity: No such file or directory

Work dir:
  /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/0e/c9cba40483c7e9397b2e23412fad15

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Sep-17 23:45:52.016 [Task monitor] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Sep-17 23:45:52.029 [main] DEBUG nextflow.Session - Session await > all process finished
Sep-17 23:45:52.041 [Actor Thread 42] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Sep-17 23:45:52.057 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1546695; id: 3; name: NFCORE_MAG:MAG:CENTRIFUGE_DB_PREPARATION; status: COMPLETED; exit: 127; error: -; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/b5/591599b985a2b2ed5f7ebe82c57a58 started: 1631936752048; exited: 2021-09-18T03:45:50.035106Z; ]
Sep-17 23:45:52.070 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1546696; id: 4; name: NFCORE_MAG:MAG:BUSCO_QC:BUSCO_DB_PREPARATION (bacteria_odb10.2020-03-06.tar); status: COMPLETED; exit: 127; error: -; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/a7/e3616a3006eaef52a57651b1b5b6be started: 1631936752062; exited: 2021-09-18T03:45:50.009915Z; ]
Sep-17 23:45:56.931 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1546697; id: 6; name: NFCORE_MAG:MAG:FASTQC_RAW (test_minigut); status: COMPLETED; exit: 127; error: -; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/fe/fb4ac7d70622167bbdf5d80c3b7632 started: 1631936756919; exited: 2021-09-18T03:45:51.143297Z; ]
Sep-17 23:46:01.930 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1546698; id: 8; name: NFCORE_MAG:MAG:FASTQC_RAW (test_minigut_sample2); status: COMPLETED; exit: 127; error: -; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/42/1315abd9abfc459b43e7162e5fd10f started: 1631936761919; exited: 2021-09-18T03:45:51.046114Z; ]
Sep-17 23:46:01.949 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1546699; id: 7; name: NFCORE_MAG:MAG:FASTP (test_minigut_sample2); status: COMPLETED; exit: 127; error: -; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/a0/ffd7f07923067fa760de2df6177b0c started: 1631936761937; exited: 2021-09-18T03:45:51.106523Z; ]
Sep-17 23:46:06.934 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1546700; id: 5; name: NFCORE_MAG:MAG:FASTP (test_minigut); status: COMPLETED; exit: 127; error: -; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/81/c3235984061abad0d5c5782ce88274 started: 1631936766919; exited: 2021-09-18T03:46:03.036714Z; ]
Sep-17 23:46:16.930 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1546693; id: 1; name: NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_BUILD (GCA_002596845.1_ASM259684v1_genomic.fna.gz); status: COMPLETED; exit: 127; error: -; workDir: /isilon/lethbridge-rdc/users/ortegapoloro/mag_test/work/a6/c6e62b1cb7526f3f26c1804af45b0d started: 1631936776919; exited: 2021-09-18T03:45:50.01064Z; ]
Sep-17 23:46:16.935 [main] DEBUG nextflow.Session - Session await > all barriers passed
Sep-17 23:46:16.953 [main] INFO  nextflow.Nextflow - -ESC[0;35m[nf-core/mag]ESC[0;31m Pipeline completed with errorsESC[0m-
Sep-17 23:46:16.962 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=8; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=144ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=2; peakMemory=6 GB; ]
Sep-17 23:46:16.962 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
Sep-17 23:46:16.966 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
Sep-17 23:46:17.028 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  [{"cpuUsage":null,"process":"KRAKEN2_DB_PREPARATION","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":19,"min":19,"q1":19,"q2":19,"q3":19,"max":19,"minLabel":"NFCORE_MAG:MAG:KRAKEN2_DB_PREPARATION","maxLabel":"NFCORE_MAG:MAG:KRAKEN2_DB_PREPARATION","q1Label":"NFCORE_MAG:MAG:KRAKEN2_DB_PREPARATION","q2Label":"NFCORE_MAG:MAG:KRAKEN2_DB_PREPARATION","q3Label":"NFCORE_MAG:MAG:KRAKEN2_DB_PREPARATION"},"writes":null},{"cpuUsage":null,"process":"CENTRIFUGE_DB_PREPARATION","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":9,"min":9,"q1":9,"q2":9,"q3":9,"max":9,"minLabel":"NFCORE_MAG:MAG:CENTRIFUGE_DB_PREPARATION","maxLabel":"NFCORE_MAG:MAG:CENTRIFUGE_DB_PREPARATION","q1Label":"NFCORE_MAG:MAG:CENTRIFUGE_DB_PREPARATION","q2Label":"NFCORE_MAG:MAG:CENTRIFUGE_DB_PREPARATION","q3Label":"NFCORE_MAG:MAG:CENTRIFUGE_DB_PREPARATION"},"writes":null},{"cpuUsage":null,"process":"BUSCO_DB_PREPARATION","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":8,"min":8,"q1":8,"q2":8,"q3":8,"max":8,"minLabel":"NFCORE_MAG:MAG:BUSCO_QC:BUSCO_DB_PREPARATION (bacteria_odb10.2020-03-06.tar)","maxLabel":"NFCORE_MAG:MAG:BUSCO_QC:BUSCO_DB_PREPARATION (bacteria_odb10.2020-03-06.tar)","q1Label":"NFCORE_MAG:MAG:BUSCO_QC:BUSCO_DB_PREPARATION (bacteria_odb10.2020-03-06.tar)","q2Label":"NFCORE_MAG:MAG:BUSCO_QC:BUSCO_DB_PREPARATION (bacteria_odb10.2020-03-06.tar)","q3Label":"NFCORE_MAG:MAG:BUSCO_QC:BUSCO_DB_PREPARATION (bacteria_odb10.2020-03-06.tar)"},"writes":null},{"cpuUsage":null,"process":"FASTQC_RAW","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":11.5,"min":11,"q1":11.25,"q2":11.5,"q3":11.75,"max":12,"minLabel":"NFCORE_MAG:MAG:FASTQC_RAW (test_minigut_sample2)","maxLabel":"NFCORE_MAG:MAG:FASTQC_RAW (test_minigut)","q1Label":"NFCORE_MAG:MAG:FASTQC_RAW (test_minigut_sample2)","q2Label":"NFCORE_MAG:MAG:FASTQC_RAW (test_minigut_sample2)","q3Label":"NFCORE_MAG:MAG:FASTQC_RAW (test_minigut_sample2)"},"writes":null},{"cpuUsage":null,"process":"FASTP","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":13,"min":12,"q1":12.5,"q2":13,"q3":13.5,"max":14,"minLabel":"NFCORE_MAG:MAG:FASTP (test_minigut_sample2)","maxLabel":"NFCORE_MAG:MAG:FASTP (test_minigut)","q1Label":"NFCORE_MAG:MAG:FASTP (test_minigut_sample2)","q2Label":"NFCORE_MAG:MAG:FASTP (test_minigut_sample2)","q3Label":"NFCORE_MAG:MAG:FASTP (test_minigut_sample2)"},"writes":null},{"cpuUsage":null,"process":"BOWTIE2_PHIX_REMOVAL_BUILD","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":10,"min":10,"q1":10,"q2":10,"q3":10,"max":10,"minLabel":"NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_BUILD (GCA_002596845.1_ASM259684v1_genomic.fna.gz)","maxLabel":"NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_BUILD (GCA_002596845.1_ASM259684v1_genomic.fna.gz)","q1Label":"NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_BUILD (GCA_002596845.1_ASM259684v1_genomic.fna.gz)","q2Label":"NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_BUILD (GCA_002596845.1_ASM259684v1_genomic.fna.gz)","q3Label":"NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_BUILD (GCA_002596845.1_ASM259684v1_genomic.fna.gz)"},"writes":null}]
Sep-17 23:46:17.992 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
Sep-17 23:46:18.726 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Sep-17 23:46:18.726 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.1.0'
Sep-17 23:46:18.726 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Sep-17 23:46:18.778 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

System

$ cat /etc/os-release
NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

Nextflow Installation

$ nextflow -version

      N E X T F L O W
      version 21.04.0 build 5552
      created 02-05-2021 16:22 UTC (12:22 EDT)
      cite doi:10.1038/nbt.3820
      http://nextflow.io

Container engine

$ singularity --version
singularity version 3.7.1

Additional context

  • This issue might be similar to this other issue in fetchngs

  • I do have a Singularity cache directory where those containers were already downloaded
@ropolomx ropolomx added the bug Something isn't working label Sep 18, 2021
@d4straub
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Hi!

The issue you mentioned, nf-core/fetchngs#12, seems to me rather because of a wrong choice of container in the pipeline script. The fix was to use another container. However, it seems to me that your problem isn't related.

To me, your issue seems to be related to nf-core/eager#68, i.e. it might be a config problem.

But I admit that I am not an expert in that matter. I will use the pipeline in the next days, and if its a container problem I will run into it too (and fix it).

If you do want to test the potential config solution, please let me know in case that works, otherwise I think I have to refer you to the nf-core slack with more knowledgeable people for that problem.

Best

@ropolomx
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Hi @d4straub ! Thank you so much for pointing me to the issue of the eager repo. Indeed this was a config problem, and I fixed this with the following in my config file. We don't have module in our cluster, and we are encouraged to use conda to activate the singularity env. This seems to work. Thank you for taking the time to look into this and replying to me!

process {
    executor = 'sge'
    clusterOptions = '-cwd -V'
    penv = 'smp'
    beforeScript = 'source ~/miniconda3/etc/profile.d/conda.sh; conda activate singularity'
}

@d4straub d4straub mentioned this issue May 12, 2023
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@ropolomx @d4straub