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PGScatalog / pgsc_calc

The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation
https://pgsc-calc.readthedocs.io/en/latest/
Apache License 2.0
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ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF when using --run_ancestry #332

Closed Carldeboer closed 2 months ago

Carldeboer commented 4 months ago

Description of the bug

Still trying to get --run_ancestry working, now encountering a new error during plink command execution:

FATAL:   container creation failed: image driver mount failure: image driver squashfuse_ll instance exited with error: squashfuse_ll

Command used and terminal output

$ nextflow run pgscatalog/pgsc_calc -r dev -latest -profile apptainer --input AF_cohort_samplesheet.hg19.cohort.txt  --target_build GRCh37 --pgs_id PGS000016,PGS002814,PGS000014,PGS002426 --outdir AF_cohort_AF_PGSs_hg19 --run_ancestry 1KG_ref/pgsc_HGDP+1kGP_v1.tar.zst

 N E X T F L O W   ~  version 24.04.2

Pulling pgscatalog/pgsc_calc ...
 Already-up-to-date
Launching `https://github.com/pgscatalog/pgsc_calc` [pensive_jennings] DSL2 - revision: ba5d0f810a [dev]

------------------------------------------------------
  pgscatalog/pgsc_calc v2.0.0-beta-gba5d0f8
------------------------------------------------------
Core Nextflow options
  revision          : dev
  runName           : pensive_jennings
  containerEngine   : apptainer
  launchDir         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank
  workDir           : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work
  projectDir        : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc
  userName          : cdeboer
  profile           : apptainer
  configFiles       :

Input/output options
  input             : AF_cohort_samplesheet.hg19.cohort.txt
  pgs_id            : PGS000016,PGS002814,PGS000014,PGS002426
  outdir            : AF_cohort_AF_PGSs_hg19

Reference options
  run_ancestry      : 1KG_ref/pgsc_HGDP+1kGP_v1.tar.zst
  ref_samplesheet   : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
  ld_grch37         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
  ld_grch38         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
  ancestry_checksums: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/assets/ancestry/checksums.txt

Compatibility options
  target_build      : GRCh37

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

* The Polygenic Score Catalog
  https://doi.org/10.1101/2024.05.29.24307783
  https://doi.org/10.1038/s41588-021-00783-5

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

* Software dependencies
  https://github.com/pgscatalog/pgsc_calc/blob/main/CITATIONS.md

Reference database provided: skipping bootstrap
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                    -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES         -
executor >  local (6)
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                                    -
executor >  local (8)
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                                     -
executor >  local (10)
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                                     -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES                          -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                       -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR                      -
[da/03fe09] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 15) [  0%] 0 of 22
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE                       [  0%] 0 of 1
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS                     -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FILTER_VARIANTS                        -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF                     -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_THINNED                      -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS                            -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_TARGET                  -
executor >  local (12)
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                                     -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES                          -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                       -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR                      -
[bb/698a53] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 13) [ 36%] 8 of 22, failed: 8
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE                       [  0%] 0 of 1
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS                     -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FILTER_VARIANTS                        -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF                     -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_THINNED                      -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS                            -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_TARGET                  -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_ORIENT                          -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA                            -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT                        -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS                                    -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE                                     -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_SCOREFILES                          -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ                               -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE                                -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE                             -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:ANCESTRY_ANALYSIS                                -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT                                     -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS                                    -
Pulling Apptainer image docker://ghcr.io/pgscatalog/pygscatalog:pgscatalog-utils-1.1.2 [cache /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/singularity/ghcr.io-pgscatalog-pygscatalog-pgscatalog-utils-1.1.2.img]
Execution cancelled -- Finishing pending tasks before exit
WARN: Apptainer cache directory has not been defined -- Remote image will be stored in the path: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/singularity -- Use the environment variable NXF_APPTAINER_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 1)'

Caused by:
  Process `PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 1)` terminated with an error exit status (255)

Command executed:

  plink2 \
      --threads 2 \
      --memory 16384 \
      --set-all-var-ids '@:#:$r:$a' \
      --max-alleles 2 \
      --freq \
      --missing vcols=fmissdosage,fmiss \
      --new-id-max-allele-len 100 missing \
      --vcf 1_af.imputed.vcf.gz  \
      --allow-extra-chr --chr 1 \
      --make-pgen vzs pvar-cols="-xheader,-maybequal,-maybefilter,-maybeinfo,-maybecm" \
      --out GRCh37_AFcohortHG19_1

  gzip GRCh37_AFcohortHG19_1.vmiss
  gzip GRCh37_AFcohortHG19_1.afreq

  cat <<-END_VERSIONS > versions.yml
  "PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF":
      plink2: $(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*$//' )
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  INFO:    gocryptfs not found, will not be able to use gocryptfs
  INFO:    A fusermount error may indicate that the kernel is too old
  INFO:    The --unsquash option may work around it
  FATAL:   container creation failed: image driver mount failure: image driver squashfuse_ll instance exited with error: squashfuse_ll exited: fusermount: mountpoint /dev/fuse is not a directory or a regular file
  cp: '.command.out' and '.command.out' are the same file
  cp: '.command.err' and '.command.err' are the same file
  cp: cannot stat '.command.trace': No such file or directory

Work dir:
  /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/6c/e7f9e4905b61e1f67635c5d9a607ac

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

 -- Check '.nextflow.log' file for details
ERROR ~ ERROR: Projection subworkflow failed

 -- Check '.nextflow.log' file for details

Relevant files

$ cat .nextflow.log
Jul-04 08:39:51.499 [main] DEBUG nextflow.cli.Launcher - $> nextflow run pgscatalog/pgsc_calc -r dev -latest -profile apptainer --input AF_cohort_samplesheet.hg19.cohort.txt --target_build GRCh37 --pgs_id PGS000016,PGS002814,PGS000014,PGS002426 --outdir AF_cohort_AF_PGSs_hg19 --run_ancestry 1KG_ref/pgsc_HGDP+1kGP_v1.tar.zst
Jul-04 08:39:51.708 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.04.2
Jul-04 08:39:51.783 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/plugins; core-plugins: nf-amazon@2.5.2,nf-azure@1.6.0,nf-cloudcache@0.4.1,nf-codecommit@0.2.0,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2,nf-tower@1.9.1,nf-wave@1.4.2
Jul-04 08:39:51.809 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-04 08:39:51.811 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-04 08:39:51.815 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Jul-04 08:39:51.860 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jul-04 08:39:51.908 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/scm
Jul-04 08:39:53.195 [main] DEBUG nextflow.scm.AssetManager - Git config: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/.git/config; branch: main; remote: origin; url: https://github.com/PGScatalog/pgsc_calc.git
Jul-04 08:39:53.241 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jul-04 08:39:53.262 [main] DEBUG nextflow.scm.AssetManager - Git config: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/.git/config; branch: main; remote: origin; url: https://github.com/PGScatalog/pgsc_calc.git
Jul-04 08:39:53.264 [main] INFO  nextflow.cli.CmdRun - Pulling pgscatalog/pgsc_calc ...
Jul-04 08:39:53.266 [main] DEBUG nextflow.scm.AssetManager - Pull pipeline pgscatalog/pgsc_calc  -- Using local path: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc
Jul-04 08:39:55.671 [main] INFO  nextflow.cli.CmdRun -  Already-up-to-date
Jul-04 08:39:55.688 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/nextflow.config
Jul-04 08:39:55.690 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/nextflow.config
Jul-04 08:39:55.700 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/secrets/store.json
Jul-04 08:39:55.703 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@61b60600] - activable => nextflow.secret.LocalSecretsProvider@61b60600
Jul-04 08:39:55.717 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `apptainer`
Jul-04 08:39:56.604 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bih, cfc_dev, uzl_omics, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, lugh, mccleary, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, arm, rosalind, hasta, cfc, uzh, ebi_codon_slurm, ebc, ccga_dx, crick, ku_sund_danhead, marvin, biohpc_gen, shifter, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, imperial, maestro, software_license, utd_europa, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, qmul_apocrita, docker, engaging, gis, hypatia, psmn, eva, nygc, fgcz, conda, crg, singularity, self_hosted_runner, tufts, uw_hyak_pedslabs, utd_sysbio, debug, genouest, cbe, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac]
Jul-04 08:39:56.657 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jul-04 08:39:56.658 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/pgscatalog/pgsc_calc` [pensive_jennings] DSL2 - revision: ba5d0f810a [dev]
Jul-04 08:39:56.660 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.0.0, nf-prov@1.2.2]
Jul-04 08:39:56.661 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-04 08:39:56.661 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.0.0, nf-prov@1.2.2]
Jul-04 08:39:56.661 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.0.0
Jul-04 08:39:56.694 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.0.0' resolved
Jul-04 08:39:56.695 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.0.0'
Jul-04 08:39:56.759 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.0.0
Jul-04 08:39:56.759 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-prov version: 1.2.2
Jul-04 08:39:56.779 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-prov@1.2.2' resolved
Jul-04 08:39:56.780 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-prov@1.2.2'
Jul-04 08:39:56.787 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-prov@1.2.2
Jul-04 08:39:56.910 [main] DEBUG nextflow.Session - Session UUID: 4c264c6e-96e7-42e3-bed0-964df9ec64d9
Jul-04 08:39:56.911 [main] DEBUG nextflow.Session - Run name: pensive_jennings
Jul-04 08:39:56.911 [main] DEBUG nextflow.Session - Executor pool size: 16
Jul-04 08:39:56.923 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jul-04 08:39:56.929 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-04 08:39:56.965 [main] DEBUG nextflow.cli.CmdRun -
  Version: 24.04.2 build 5914
  Created: 29-05-2024 06:19 UTC (28-05-2024 23:19 PDT)
  System: Linux 5.14.0-362.24.1.el9_3.0.1.x86_64
  Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 11.0.13+7-b1751.21
  Encoding: UTF-8 (UTF-8)
  Process: 2054330@login01 [206.12.119.243]
  CPUs: 16 - Mem: 187.5 GB (29.3 GB) - Swap: 0 (0)
Jul-04 08:39:57.006 [main] DEBUG nextflow.Session - Work-dir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work [nfs]
Jul-04 08:39:57.007 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/bin
Jul-04 08:39:57.061 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-04 08:39:57.077 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-04 08:39:57.102 [main] DEBUG nextflow.Session - Observer factory: ProvObserverFactory
Jul-04 08:39:57.261 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-04 08:39:57.284 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 17; maxThreads: 1000
Jul-04 08:39:57.651 [main] DEBUG nextflow.Session - Session start
Jul-04 08:39:57.655 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/AF_cohort_AF_PGSs_hg19/pipeline_info/execution_trace_2024-07-04_08-39-56.txt
Jul-04 08:39:57.670 [main] DEBUG nextflow.Session - Using default localLib path: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/lib
Jul-04 08:39:57.679 [main] DEBUG nextflow.Session - Adding to the classpath library: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/lib
Jul-04 08:39:58.160 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-04 08:39:58.175 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema
Jul-04 08:39:58.887 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters, paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
Jul-04 08:39:59.011 [main] INFO  nextflow.Nextflow -

------------------------------------------------------
  pgscatalog/pgsc_calc v2.0.0-beta-gba5d0f8
------------------------------------------------------
Core Nextflow options
  revision          : dev
  runName           : pensive_jennings
  containerEngine   : apptainer
  launchDir         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank
  workDir           : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work
  projectDir        : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc
  userName          : cdeboer
  profile           : apptainer
  configFiles       :

Input/output options
  input             : AF_cohort_samplesheet.hg19.cohort.txt
  pgs_id            : PGS000016,PGS002814,PGS000014,PGS002426
  outdir            : AF_cohort_AF_PGSs_hg19

Reference options
  run_ancestry      : 1KG_ref/pgsc_HGDP+1kGP_v1.tar.zst
  ref_samplesheet   : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
  ld_grch37         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
  ld_grch38         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
  ancestry_checksums: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/assets/ancestry/checksums.txt

Compatibility options
  target_build      : GRCh37

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

* The Polygenic Score Catalog
  https://doi.org/10.1101/2024.05.29.24307783
  https://doi.org/10.1038/s41588-021-00783-5

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

* Software dependencies
  https://github.com/pgscatalog/pgsc_calc/blob/main/CITATIONS.md

Jul-04 08:40:04.322 [main] INFO  nextflow.Nextflow - Reference database provided: skipping bootstrap
Jul-04 08:40:04.515 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES
Jul-04 08:40:04.516 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES
Jul-04 08:40:04.530 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-04 08:40:04.530 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-04 08:40:04.538 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jul-04 08:40:04.547 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=16; memory=187.5 GB; capacity=16; pollInterval=100ms; dumpInterval=5m
Jul-04 08:40:04.551 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jul-04 08:40:04.758 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES
Jul-04 08:40:04.759 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES
Jul-04 08:40:04.760 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COMBINE_SCOREFILES` matches process PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES
Jul-04 08:40:04.762 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-04 08:40:04.762 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-04 08:40:04.839 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM
Jul-04 08:40:04.840 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM
Jul-04 08:40:04.841 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_RELABELBIM` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM
Jul-04 08:40:04.848 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-04 08:40:04.849 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-04 08:40:04.876 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR
Jul-04 08:40:04.877 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR
Jul-04 08:40:04.877 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_RELABELPVAR` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR
Jul-04 08:40:04.880 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-04 08:40:04.880 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-04 08:40:04.900 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF
Jul-04 08:40:04.901 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_medium,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF
Jul-04 08:40:04.902 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_VCF` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF
Jul-04 08:40:04.905 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-04 08:40:04.905 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-04 08:40:04.987 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,zstd` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE
Jul-04 08:40:04.987 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:zstd` matches labels `process_low,zstd` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE
Jul-04 08:40:04.991 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-04 08:40:04.991 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-04 08:40:05.052 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS
Jul-04 08:40:05.053 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_single,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS
Jul-04 08:40:05.055 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-04 08:40:05.055 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-04 08:40:05.106 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FILTER_VARIANTS
Jul-04 08:40:05.107 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FILTER_VARIANTS
Jul-04 08:40:05.111 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-04 08:40:05.111 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-04 08:40:05.137 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF
Jul-04 08:40:05.139 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF
Jul-04 08:40:05.142 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-04 08:40:05.142 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-04 08:40:05.173 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_high_memory,process_long,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_THINNED
Jul-04 08:40:05.173 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,process_long,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_THINNED
Jul-04 08:40:05.173 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_high_memory,process_long,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_THINNED
J
... I deleted a lot from the middle because it was over the character limit...

  Script_6959f3d68143b55a: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/fraposa_project.nf
  Script_6c7f1975e3fb3b69: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/fraposa_pca.nf
  Script_ac673998bae353b8: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/intersect_variants.nf
  Script_f7e6cf6aaa57ea1f: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/ancestry/ancestry_analysis.nf
  Script_3192a83c982d60fd: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/ancestry/relabel_afreq.nf
  Script_427b79f8ec452926: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/extract_database.nf
  Script_a9598b3d758285aa: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/score_aggregate.nf
  Script_951dc19390c5c741: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/combine_scorefiles.nf
  Script_1317eccf6cefc502: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/ancestry_project.nf
  Script_12c9a6a07f86b4fa: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../modules/local/download_scorefiles.nf
  Script_a1b2ac31471479b0: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/pgsc_calc.nf
  Script_67ef02006e15f7bf: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/bootstrap/make_database.nf
  Script_85d9c5de3f9419f5: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_score.nf
  Script_e72266e4c23a6709: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/bootstrap_ancestry.nf
  Script_49dad12165a607ad: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/main.nf
  Script_af7d999c868fc751: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/plink2_relabelpvar.nf
  Script_7877cbba589aaba3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_relabelbim.nf
  Script_ddfebfdd3f2163fa: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/intersect_thinned.nf
  Script_0fa47898366f4cc3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/make_compatible.nf
  Script_e8e89f1db16463e9: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/input_check.nf
  Script_dac204016b7d984d: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/match_combine.nf
  Script_71125e7d812b2828: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/apply_score.nf
  Script_f7586381070cd5d9: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_vcf.nf
  Script_7471b788f1a2a9d3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/filter_variants.nf
  Script_58fbd5e82e3df7c9: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/report.nf
  Script_a1be163d058c7f54: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../modules/local/dumpsoftwareversions.nf
  Script_5556e4a34f537c27: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/match.nf
  Script_b5a82ee5e9eb54e0: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/plink2_makebed.nf
  Script_dfec6a09ab0763d3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/score_report.nf
  Script_7237b9b1d4f9edb3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/bootstrap/setup_resource.nf
  Script_27f93d0e8e1609f8: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/match_variants.nf
  Script_75119a130470a3ec: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/plink2_orient.nf
  Script_8e039f797b24a3eb: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/ancestry/relabel_scorefiles.nf
  Script_9484cf4d32ea80d5: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines3/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/relabel_ids.nf
Jul-04 08:40:05.675 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jul-04 08:40:05.675 [main] DEBUG nextflow.Session - Session await
Jul-04 08:40:05.841 [Actor Thread 28] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://ghcr.io/pgscatalog/plink2:2.00a5.10; path=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/singularity/ghcr.io-pgscatalog-plink2-2.00a5.10.img
Jul-04 08:40:05.841 [Actor Thread 25] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/zstd:1.4.8; path=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/singularity/dockerhub.ebi.ac.uk-gdp-public-pgsc_calc-zstd-1.4.8.img
Jul-04 08:40:05.847 [Actor Thread 12] WARN  nextflow.container.SingularityCache - Apptainer cache directory has not been defined -- Remote image will be stored in the path: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/singularity -- Use the environment variable NXF_APPTAINER_CACHEDIR to specify a different location
Jul-04 08:40:05.851 [Actor Thread 12] INFO  nextflow.container.SingularityCache - Pulling Apptainer image docker://ghcr.io/pgscatalog/pygscatalog:pgscatalog-utils-1.1.2 [cache /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/singularity/ghcr.io-pgscatalog-pygscatalog-pgscatalog-utils-1.1.2.img]
Jul-04 08:40:06.042 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-04 08:40:06.044 [Task submitter] INFO  nextflow.Session - [6c/e7f9e4] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 1)
Jul-04 08:40:06.063 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-04 08:40:06.064 [Task submitter] INFO  nextflow.Session - [11/d4cdd4] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 3)
Jul-04 08:40:06.080 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-04 08:40:06.081 [Task submitter] INFO  nextflow.Session - [1a/afdc6d] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 14)
Jul-04 08:40:06.102 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-04 08:40:06.103 [Task submitter] INFO  nextflow.Session - [98/4f5d86] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 16)
Jul-04 08:40:06.143 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-04 08:40:06.144 [Task submitter] INFO  nextflow.Session - [f7/19b1c9] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 12)
Jul-04 08:40:06.171 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-04 08:40:06.172 [Task submitter] INFO  nextflow.Session - [0d/c4fb49] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 6)
Jul-04 08:40:06.204 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-04 08:40:06.204 [Task submitter] INFO  nextflow.Session - [a4/a84c94] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 7)
Jul-04 08:40:06.276 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-04 08:40:06.277 [Task submitter] INFO  nextflow.Session - [fb/9a1936] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 11)
Jul-04 08:40:06.657 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 1); status: COMPLETED; exit: 255; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/6c/e7f9e4905b61e1f67635c5d9a607ac]
Jul-04 08:40:06.659 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-04 08:40:06.664 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 3); status: COMPLETED; exit: 255; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/11/d4cdd4df75bd327b3e19011418fdbe]
Jul-04 08:40:06.666 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 1); work-dir=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/6c/e7f9e4905b61e1f67635c5d9a607ac
  error [nextflow.exception.ProcessFailedException]: Process `PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 1)` terminated with an error exit status (255)
Jul-04 08:40:06.668 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 14); status: COMPLETED; exit: 255; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/1a/afdc6dd03d58f53db875def14402f5]
Jul-04 08:40:06.673 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 16); status: COMPLETED; exit: 255; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/98/4f5d868c85fa2325152a582bc4766c]
Jul-04 08:40:06.678 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-04 08:40:06.679 [Task submitter] INFO  nextflow.Session - [66/a025af] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 9)
Jul-04 08:40:06.679 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 12); status: COMPLETED; exit: 255; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/f7/19b1c92a90abe3721bbdb88d457869]
Jul-04 08:40:06.703 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 6); status: COMPLETED; exit: 255; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/0d/c4fb49e5dce363c09e84ea7533e916]
Jul-04 08:40:06.708 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 7); status: COMPLETED; exit: 255; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/a4/a84c9441ef0ae40c25a2f83b9c8432]
Jul-04 08:40:06.714 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 11); status: COMPLETED; exit: 255; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/fb/9a19360519897bd6ee6dec56918828]
Jul-04 08:40:06.717 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-04 08:40:06.718 [Task submitter] INFO  nextflow.Session - [da/03fe09] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 15)
Jul-04 08:40:06.719 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 1)'

Caused by:
  Process `PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 1)` terminated with an error exit status (255)

Command executed:

  plink2 \
      --threads 2 \
      --memory 16384 \
      --set-all-var-ids '@:#:$r:$a' \
      --max-alleles 2 \
      --freq \
      --missing vcols=fmissdosage,fmiss \
      --new-id-max-allele-len 100 missing \
      --vcf 1_af.imputed.vcf.gz  \
      --allow-extra-chr --chr 1 \
      --make-pgen vzs pvar-cols="-xheader,-maybequal,-maybefilter,-maybeinfo,-maybecm" \
      --out GRCh37_AFcohortHG19_1

  gzip GRCh37_AFcohortHG19_1.vmiss
  gzip GRCh37_AFcohortHG19_1.afreq

  cat <<-END_VERSIONS > versions.yml
  "PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF":
      plink2: $(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*$//' )
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  INFO:    gocryptfs not found, will not be able to use gocryptfs
  INFO:    A fusermount error may indicate that the kernel is too old
  INFO:    The --unsquash option may work around it
  FATAL:   container creation failed: image driver mount failure: image driver squashfuse_ll instance exited with error: squashfuse_ll exited: fusermount: mountpoint /dev/fuse is not a directory or a regular file
  cp: '.command.out' and '.command.out' are the same file
  cp: '.command.err' and '.command.err' are the same file
  cp: cannot stat '.command.trace': No such file or directory

Work dir:
  /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/6c/e7f9e4905b61e1f67635c5d9a607ac

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Jul-04 08:40:06.721 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 11); work-dir=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/fb/9a19360519897bd6ee6dec56918828
  error [nextflow.exception.ProcessFailedException]: Process `PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 11)` terminated with an error exit status (255)
Jul-04 08:40:06.722 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 7); work-dir=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/a4/a84c9441ef0ae40c25a2f83b9c8432
  error [nextflow.exception.ProcessFailedException]: Process `PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 7)` terminated with an error exit status (255)
Jul-04 08:40:06.723 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 6); work-dir=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/0d/c4fb49e5dce363c09e84ea7533e916
  error [nextflow.exception.ProcessFailedException]: Process `PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 6)` terminated with an error exit status (255)
Jul-04 08:40:06.729 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 12); work-dir=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/f7/19b1c92a90abe3721bbdb88d457869
  error [nextflow.exception.ProcessFailedException]: Process `PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 12)` terminated with an error exit status (255)
Jul-04 08:40:06.730 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 16); work-dir=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/98/4f5d868c85fa2325152a582bc4766c
  error [nextflow.exception.ProcessFailedException]: Process `PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 16)` terminated with an error exit status (255)
Jul-04 08:40:06.731 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 14); work-dir=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/1a/afdc6dd03d58f53db875def14402f5
  error [nextflow.exception.ProcessFailedException]: Process `PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 14)` terminated with an error exit status (255)
Jul-04 08:40:06.732 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 3); work-dir=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/11/d4cdd4df75bd327b3e19011418fdbe
  error [nextflow.exception.ProcessFailedException]: Process `PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 3)` terminated with an error exit status (255)
Jul-04 08:40:06.744 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-04 08:40:06.744 [Task submitter] INFO  nextflow.Session - [79/58c13a] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 2)
Jul-04 08:40:06.762 [TaskFinalizer-1] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Jul-04 08:40:06.781 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-04 08:40:06.782 [Task submitter] INFO  nextflow.Session - [bb/698a53] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 13)
Jul-04 08:40:06.786 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-04 08:40:06.797 [Actor Thread 13] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-04 08:40:06.799 [Actor Thread 19] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-04 08:40:06.832 [Actor Thread 3] ERROR nextflow.Nextflow - ERROR: Projection subworkflow failed
Jul-04 08:40:06.835 [Actor Thread 14] ERROR nextflow.Nextflow - ERROR: No results report written!
Jul-04 08:40:06.837 [Actor Thread 13] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-04 08:40:06.839 [Actor Thread 11] ERROR nextflow.Nextflow - ERROR: Matching subworkflow failed
Jul-04 08:40:06.843 [Actor Thread 16] ERROR nextflow.Nextflow - ERROR: No scores calculated!
Jul-04 08:40:06.848 [Actor Thread 4] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null

System information

N E X T F L O W ~ version 24.04.2 HPC local singularity linux pgsc_calc v2.0.0-beta-gba5d0f8

nebfield commented 4 months ago

Are you able to use the conda profile? These problems are caused by the way apptainer is set up on your cluster - perhaps your cluster admins can help.

Carldeboer commented 4 months ago

The error

container creation failed: image driver mount failure: image driver squashfuse_ll instance exited with error: squashfuse_ll exited: fusermount: mountpoint /dev/fuse is not a directory or a regular file

Seems to be related to this issue. Can you suggest a minimal apptainer command that would be able to reproduce the error directly?

In the mean time I will try the conda profile.

nebfield commented 4 months ago

/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/6c/e7f9e4905b61e1f67635c5d9a607ac/.command.run will contain a bash script generated by Nextflow for the failing process. The nxf_launch() function should contain the apptainer command that's failing, which might be enough for a minimal reproducible example. Good luck!

nebfield commented 2 months ago

Closing this now. Please feel free to reopen or create a new issue or discussion if you have any more questions.