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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
104 stars 18 forks source link

ERROR ~ No signature of method: java.lang.Boolean.getFileSystem() is applicable for argument types: () values: [] when using --run_ancestry #324

Open Carldeboer opened 1 week ago

Carldeboer commented 1 week ago

Description of the bug

Apologies for rapid-fire bug reports. Trying to churn this analysis out before I get too busy to complete it.

The --run_ancestry function appears to not work on my system and returns a cryptic error message.

Command used and terminal output

$ nextflow run pgscatalog/pgsc_calc -profile apptainer --input AF_cohort_samplesheet.hg19.CD.txt  --target_build GRCh37 --pgs_id PGS000016,PGS002814 --outdir AF_cohort_AF_PGSs_hg19
... works
$ nextflow run pgscatalog/pgsc_calc -profile apptainer --input AF_cohort_samplesheet.hg19.CD.txt  --target_build GRCh37 --pgs_id PGS000016,PGS002814 --outdir AF_cohort_AF_PGSs_hg19 --run_ancestry

 N E X T F L O W   ~  version 24.04.2

NOTE: Your local project version looks outdated - a different revision is available in the remote repository [ca334fa575]
Launching `https://github.com/pgscatalog/pgsc_calc` [condescending_baekeland] DSL2 - revision: 45326ac066 [main]

WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`

------------------------------------------------------
  pgscatalog/pgsc_calc v2.0.0-alpha.6-g45326ac
------------------------------------------------------
Core Nextflow options
  revision          : main
  runName           : condescending_baekeland
  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-pipelines2/assets/pgscatalog/pgsc_calc
  userName          : cdeboer
  profile           : apptainer
  configFiles       :

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

Reference options
  run_ancestry      : true
  ref_samplesheet   : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
  ld_grch37         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
  ld_grch38         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
  ancestry_checksums: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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/10.1038/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/master/CITATIONS.md

Reference database provided: skipping bootstrap
[-        ] 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     -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF             -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE      -
[-        ] 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                   -
ERROR ~ No signature of method: java.lang.Boolean.getFileSystem() is applicable for argument types: () values: []

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

 -- Check '.nextflow.log' file for details
ERROR ~ ERROR: No results report written!

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

 -- Check '.nextflow.log' file for details
ERROR ~ ERROR: No scores calculated!

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

Relevant files


$ cat .nextflow.log
Jun-19 13:33:36.773 [main] DEBUG nextflow.cli.Launcher - $> nextflow run pgscatalog/pgsc_calc -profile apptainer --input AF_cohort_samplesheet.hg19.CD.txt --target_build GRCh37 --pgs_id PGS000016,PGS002814 --outdir AF_cohort_AF_PGSs_hg19 --run_ancestry
Jun-19 13:33:36.966 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.04.2
Jun-19 13:33:36.997 [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-pipelines2/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
Jun-19 13:33:37.018 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-19 13:33:37.020 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-19 13:33:37.025 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Jun-19 13:33:37.048 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jun-19 13:33:37.069 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/scm
Jun-19 13:33:38.307 [main] DEBUG nextflow.scm.AssetManager - Git config: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/.git/config; branch: main; remote: origin; url: https://github.com/PGScatalog/pgsc_calc.git
Jun-19 13:33:38.348 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jun-19 13:33:38.364 [main] DEBUG nextflow.scm.AssetManager - Git config: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/.git/config; branch: main; remote: origin; url: https://github.com/PGScatalog/pgsc_calc.git
Jun-19 13:33:39.281 [main] INFO  nextflow.scm.AssetManager - NOTE: Your local project version looks outdated - a different revision is available in the remote repository [ca334fa575]
Jun-19 13:33:39.292 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/nextflow.config
Jun-19 13:33:39.295 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/nextflow.config
Jun-19 13:33:39.303 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/secrets/store.json
Jun-19 13:33:39.306 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@1f884bd6] - activable => nextflow.secret.LocalSecretsProvider@1f884bd6
Jun-19 13:33:39.318 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `apptainer`
Jun-19 13:33:40.250 [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, ku_sund_dangpu, ccga_dx, crick, 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]
Jun-19 13:33:40.305 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jun-19 13:33:40.306 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/pgscatalog/pgsc_calc` [condescending_baekeland] DSL2 - revision: 45326ac066 [main]
Jun-19 13:33:40.308 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-19 13:33:40.309 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jun-19 13:33:40.400 [main] DEBUG nextflow.Session - Session UUID: 5f7a8cf2-90e6-4cb1-bc5f-03092ec11532
Jun-19 13:33:40.401 [main] DEBUG nextflow.Session - Run name: condescending_baekeland
Jun-19 13:33:40.401 [main] DEBUG nextflow.Session - Executor pool size: 16
Jun-19 13:33:40.413 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jun-19 13:33:40.421 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-19 13:33:40.458 [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 3.10.0-1160.108.1.el7.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: 220062@login02 [206.12.119.244]
  CPUs: 16 - Mem: 187.5 GB (56 GB) - Swap: 0 (0)
Jun-19 13:33:40.498 [main] DEBUG nextflow.Session - Work-dir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work [nfs]
Jun-19 13:33:40.499 [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-pipelines2/assets/pgscatalog/pgsc_calc/bin
Jun-19 13:33:40.516 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-19 13:33:40.533 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-19 13:33:40.648 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-19 13:33:40.668 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 17; maxThreads: 1000
Jun-19 13:33:40.808 [main] DEBUG nextflow.Session - Session start
Jun-19 13:33:40.811 [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_2024-06-19_13-33-40.txt
Jun-19 13:33:40.825 [main] DEBUG nextflow.Session - Using default localLib path: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/lib
Jun-19 13:33:40.835 [main] DEBUG nextflow.Session - Adding to the classpath library: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/lib
Jun-19 13:33:41.483 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-19 13:33:42.296 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: latest
Jun-19 13:33:42.533 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-validation@1.1.3' resolved
Jun-19 13:33:42.533 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-validation@1.1.3'
Jun-19 13:33:42.552 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-validation@1.1.3
Jun-19 13:33:42.553 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation
Jun-19 13:33:42.632 [main] WARN  nextflow.script.ScriptBinding - Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`
Jun-19 13:33:42.639 [main] INFO  nextflow.Nextflow -

------------------------------------------------------
  pgscatalog/pgsc_calc v2.0.0-alpha.6-g45326ac
------------------------------------------------------
Core Nextflow options
  revision          : main
  runName           : condescending_baekeland
  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-pipelines2/assets/pgscatalog/pgsc_calc
  userName          : cdeboer
  profile           : apptainer
  configFiles       :

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

Reference options
  run_ancestry      : true
  ref_samplesheet   : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
  ld_grch37         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
  ld_grch38         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
  ancestry_checksums: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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/10.1038/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/master/CITATIONS.md

Jun-19 13:33:48.130 [main] INFO  nextflow.Nextflow - Reference database provided: skipping bootstrap
Jun-19 13:33:48.224 [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
Jun-19 13:33:48.225 [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
Jun-19 13:33:48.239 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:48.239 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:48.247 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jun-19 13:33:48.255 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=16; memory=187.5 GB; capacity=16; pollInterval=100ms; dumpInterval=5m
Jun-19 13:33:48.258 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jun-19 13:33:48.454 [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
Jun-19 13:33:48.454 [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
Jun-19 13:33:48.456 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COMBINE_SCOREFILES` matches process PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES
Jun-19 13:33:48.461 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:48.461 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:48.546 [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
Jun-19 13:33:48.547 [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
Jun-19 13:33:48.548 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_RELABELBIM` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM
Jun-19 13:33:48.556 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:48.556 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:48.585 [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
Jun-19 13:33:48.585 [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
Jun-19 13:33:48.586 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_RELABELPVAR` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR
Jun-19 13:33:48.589 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:48.589 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:48.611 [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
Jun-19 13:33:48.613 [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
Jun-19 13:33:48.613 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_VCF` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF
Jun-19 13:33:48.617 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:48.617 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:48.694 [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
Jun-19 13:33:48.695 [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
Jun-19 13:33:48.698 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:48.698 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:48.765 [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
Jun-19 13:33:48.765 [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
Jun-19 13:33:48.768 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:48.768 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:48.813 [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
Jun-19 13:33:48.813 [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
Jun-19 13:33:48.818 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:48.818 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:48.846 [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
Jun-19 13:33:48.850 [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
Jun-19 13:33:48.853 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:48.853 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:48.889 [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
Jun-19 13:33:48.889 [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
Jun-19 13:33:48.889 [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
Jun-19 13:33:48.892 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:48.892 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:48.908 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS
Jun-19 13:33:48.908 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS
Jun-19 13:33:48.911 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:48.911 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:48.934 [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_TARGET
Jun-19 13:33:48.935 [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_TARGET
Jun-19 13:33:48.938 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:48.938 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:48.967 [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_ORIENT
Jun-19 13:33:48.968 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_ORIENT
Jun-19 13:33:48.971 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:48.972 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:49.001 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,fraposa` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA
Jun-19 13:33:49.002 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:fraposa` matches labels `process_high_memory,fraposa` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA
Jun-19 13:33:49.004 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:49.004 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:49.029 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,fraposa` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT
Jun-19 13:33:49.030 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:fraposa` matches labels `process_high_memory,fraposa` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT
Jun-19 13:33:49.032 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:49.033 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:49.077 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-19 13:33:49.078 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-19 13:33:49.079 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MATCH_VARIANTS|MATCH_COMBINE` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-19 13:33:49.083 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:49.083 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:49.125 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-19 13:33:49.126 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-19 13:33:49.127 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MATCH_VARIANTS|MATCH_COMBINE` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-19 13:33:49.129 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:49.129 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:49.199 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_SCOREFILES
Jun-19 13:33:49.199 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_SCOREFILES
Jun-19 13:33:49.202 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:49.203 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:49.232 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ
Jun-19 13:33:49.233 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ
Jun-19 13:33:49.235 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:49.236 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:49.258 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-19 13:33:49.259 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-19 13:33:49.259 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-19 13:33:49.260 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-19 13:33:49.260 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_SCORE` matches process PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-19 13:33:49.262 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:49.262 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:49.295 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE
Jun-19 13:33:49.296 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_high_memory,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE
Jun-19 13:33:49.298 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:49.298 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:49.346 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:ANCESTRY_ANALYSIS
Jun-19 13:33:49.347 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_low,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:ANCESTRY_ANALYSIS
Jun-19 13:33:49.349 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:49.349 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:49.390 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,report` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-19 13:33:49.394 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:report` matches labels `process_high_memory,report` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-19 13:33:49.395 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PGSCATALOG_GET|SCORE_REPORT` matches process PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-19 13:33:49.397 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:49.397 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:49.441 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pyyaml` matches labels `pyyaml` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS
Jun-19 13:33:49.441 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DUMPSOFTWAREVERSIONS` matches process PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS
Jun-19 13:33:49.444 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 13:33:49.444 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 13:33:49.448 [main] DEBUG nextflow.Session - Config process names validation disabled as requested
Jun-19 13:33:49.451 [main] DEBUG nextflow.Session - Igniting dataflow network (51)
Jun-19 13:33:49.462 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES
Jun-19 13:33:49.464 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES
Jun-19 13:33:49.468 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM
Jun-19 13:33:49.469 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR
Jun-19 13:33:49.469 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF
Jun-19 13:33:49.471 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE
Jun-19 13:33:49.471 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS
Jun-19 13:33:49.472 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FILTER_VARIANTS
Jun-19 13:33:49.472 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF
Jun-19 13:33:49.473 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_THINNED
Jun-19 13:33:49.473 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS
Jun-19 13:33:49.473 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_TARGET
Jun-19 13:33:49.473 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_ORIENT
Jun-19 13:33:49.473 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA
Jun-19 13:33:49.473 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT
Jun-19 13:33:49.478 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-19 13:33:49.478 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-19 13:33:49.478 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_SCOREFILES
Jun-19 13:33:49.478 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ
Jun-19 13:33:49.478 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-19 13:33:49.479 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE
Jun-19 13:33:49.480 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:ANCESTRY_ANALYSIS
Jun-19 13:33:49.480 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-19 13:33:49.481 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS
Jun-19 13:33:49.487 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_ac673998bae353b8: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/intersect_variants.nf
  Script_4b4c11c4fe56d274: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/match_variants.nf
  Script_427b79f8ec452926: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/extract_database.nf
  Script_6ee8db14b0ece2bc: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/main.nf
  Script_b4ded561a904b4b9: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/pgsc_calc.nf
  Script_a9598b3d758285aa: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/score_aggregate.nf
  Script_951dc19390c5c741: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/combine_scorefiles.nf
  Script_1317eccf6cefc502: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/ancestry_project.nf
  Script_12c9a6a07f86b4fa: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../modules/local/download_scorefiles.nf
  Script_c7b87f734d3160d0: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/fraposa_project.nf
  Script_67ef02006e15f7bf: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_score.nf
  Script_e72266e4c23a6709: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/bootstrap_ancestry.nf
  Script_0590bc8b268609ac: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/relabel_ids.nf
  Script_dd9e9d3067ae34d9: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_vcf.nf
  Script_7877cbba589aaba3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_relabelbim.nf
  Script_fd7831fa32f2ed40: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/ancestry/relabel_afreq.nf
  Script_ddfebfdd3f2163fa: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/make_compatible.nf
  Script_1325f56916418255: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_relabelpvar.nf
  Script_e8e89f1db16463e9: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/input_check.nf
  Script_dac204016b7d984d: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/match_combine.nf
  Script_71125e7d812b2828: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/apply_score.nf
  Script_8463068cf880c25a: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/ancestry/ancestry_analysis.nf
  Script_7471b788f1a2a9d3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/report.nf
  Script_a1be163d058c7f54: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../modules/local/dumpsoftwareversions.nf
  Script_5556e4a34f537c27: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/match.nf
  Script_b5a82ee5e9eb54e0: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/score_report.nf
  Script_7237b9b1d4f9edb3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/bootstrap/setup_resource.nf
  Script_00d09c28a4e6e597: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/ancestry/relabel_scorefiles.nf
  Script_75119a130470a3ec: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/plink2_orient.nf
  Script_1c509e4a65296f87: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/fraposa_pca.nf
Jun-19 13:33:49.489 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jun-19 13:33:49.489 [main] DEBUG nextflow.Session - Session await
Jun-19 13:33:49.536 [PathVisitor-1] ERROR nextflow.Channel - No signature of method: java.lang.Boolean.getFileSystem() is applicable for argument types: () values: []
org.codehaus.groovy.runtime.metaclass.MissingMethodExceptionNoStack: No signature of method: java.lang.Boolean.getFileSystem() is applicable for argument types: () values: []
Jun-19 13:33:49.563 [PathVisitor-1] DEBUG nextflow.Session - Session aborted -- Cause: No signature of method: java.lang.Boolean.getFileSystem() is applicable for argument types: () values: []
Jun-19 13:33:49.574 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jun-19 13:33:49.635 [PathVisitor-1] DEBUG nextflow.Session - The following nodes are still active:
[process] PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES
  status=ACTIVE
  port 0: (value) bound ; channel: meta
  port 1: (value) bound ; channel: build
  port 2: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES
  status=ACTIVE
  port 0: (value) OPEN  ; channel: raw_scores
  port 1: (queue) OPEN  ; channel: reference
  port 2: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: reference
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FILTER_VARIANTS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_THINNED
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_TARGET
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_ORIENT
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (queue) OPEN  ; channel: -
  port 2: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_SCOREFILES
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE
  status=ACTIVE
  port 0: (value) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:ANCESTRY_ANALYSIS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: intersect_count
  port 2: (queue) OPEN  ; channel: reference_panel_name
  port 3: (queue) OPEN  ; channel: report_path
  port 4: (cntrl) -     ; channel: $

[process] PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: versions
  port 1: (cntrl) -     ; channel: $

Jun-19 13:33:49.656 [main] DEBUG nextflow.Session - Session await > all processes finished
Jun-19 13:33:49.656 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jun-19 13:33:49.667 [Actor Thread 27] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://ghcr.io/pgscatalog/pygscatalog:pgscatalog-utils-1.0.2; path=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/singularity/ghcr.io-pgscatalog-pygscatalog-pgscatalog-utils-1.0.2.img
Jun-19 13:33:49.674 [Actor Thread 20] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF; work-dir=null
  error [java.lang.IllegalStateException]: Cannot obtain the semaphore to fork operator's body.
Jun-19 13:33:49.678 [Actor Thread 12] 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
Jun-19 13:33:49.688 [Actor Thread 23] ERROR nextflow.Nextflow - ERROR: Matching subworkflow failed
Jun-19 13:33:49.688 [Actor Thread 37] ERROR nextflow.Nextflow - ERROR: No results report written!
Jun-19 13:33:49.713 [Actor Thread 24] ERROR nextflow.Nextflow - ERROR: Projection subworkflow failed
Jun-19 13:33:49.713 [Actor Thread 36] ERROR nextflow.Nextflow - ERROR: No scores calculated!
Jun-19 13:33:49.719 [Actor Thread 27] 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
apptainer
linux
latest pgsc_calc
smlmbrt commented 1 week ago

Could you try the new version v2.0.0-beta? We ended up downgrading alpha.6 because it was unstable.

Carldeboer commented 1 week ago

I tried but it couldn't seem to find that version:

$ nextflow clone pgscatalog/pgsc_calc -r v2.0.0-beta
Cloning pgscatalog/pgsc_calc:v2.0.0-beta ...Remote branch 'v2.0.0-beta' not found in upstream origin
smlmbrt commented 1 week ago

Hmmm, that's one for @nebfield! You can try -r main -latest instead and that should get you there too?

Carldeboer commented 1 week ago

Can you give the exact command to use? I tried this and some variations of it but couldnt figure out what exactly I should do:

$ nextflow clone pgscatalog/pgsc_calc -r main -latest
Unknown option: -latest -- Check the available commands and options and syntax with 'help'
Carldeboer commented 1 week ago

I moved the cached version of pgsc_calc and when it re-downloaded it was 2.0.0-beta - same issue though

$ nextflow run pgscatalog/pgsc_calc -profile apptainer --input AF_cohort_samplesheet.hg19.CD.txt  --target_build GRCh37 --pgs_id PGS000016,PGS002814 --outdir AF_cohort_AF_PGSs_hg19 --run_ancestry

 N E X T F L O W   ~  version 24.04.2

Pulling pgscatalog/pgsc_calc ...
 downloaded from https://github.com/PGScatalog/pgsc_calc.git
Launching `https://github.com/pgscatalog/pgsc_calc` [jovial_turing] DSL2 - revision: ca334fa575 [main]

Downloading plugin nf-schema@2.0.0
Downloading plugin nf-prov@1.2.2

------------------------------------------------------
  pgscatalog/pgsc_calc v2.0.0-beta-gca334fa
------------------------------------------------------
Core Nextflow options
  revision          : main
  runName           : jovial_turing
  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-pipelines2/assets/pgscatalog/pgsc_calc
  userName          : cdeboer
  profile           : apptainer
  configFiles       :

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

Reference options
  run_ancestry      : true
  ref_samplesheet   : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
  ld_grch37         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
  ld_grch38         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
  ancestry_checksums: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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         -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM      -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR     -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF             -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE      -
[-        ] 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                   -
ERROR ~ No signature of method: java.lang.Boolean.getFileSystem() is applicable for argument types: () values: []

 -- Check '.nextflow.log' file for details
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (5)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (12)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (6)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (13)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (2)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (11)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (14)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (10)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (15)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (7)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (9)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (1)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (8)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (3)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (4)
[skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (16)
ERROR ~ ERROR: Projection subworkflow failed

 -- Check '.nextflow.log' file for details
ERROR ~ ERROR: No scores calculated!

 -- Check '.nextflow.log' file for details
ERROR ~ ERROR: No results report written!

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

 -- Check '.nextflow.log' file for details
nebfield commented 1 week ago

Thanks for the bug report! Could you share the latest .nextflow.log file you get when you run the beta release?

I did encounter this problem on a HPC but temporarily disabling this fixed the problem for me 🤔 (it's disabled by default in the release)

Also, can I double check if you're providing --run_ancestry with a valid path to a reference database?

Carldeboer commented 1 week ago

Haha... no. I wasn't giving it a reference database! I was trying to follow the instructions here and never saw that it needed one. I'll download a reference and get back to you.

When using a reference panel, is the reference subset to the genoptypes of the cohort somehow? I'm already encountering issues with my two cohorts who were genotyped and imputed separately and therefore don't have the same SNPs and thus also don't have comparable scores. I'm wondering if this could help solve it by having both expressed as a Z score to the same reference.

nebfield commented 1 week ago

The variants in the reference panel are intersected with the variants in your target genomes using pgscatalog-intersect. The intersection is used to select a subset of PCA eligible variants and to constrain matches against variants in the scoring file, so scores are calculated for the target genomes and reference panel using the same set of variants.

smlmbrt commented 1 week ago

I'm wondering if this could help solve it by having both expressed as a Z score to the same reference.

Yes, this is part of the motivation behind the ancestry analyses. The Z-scores will be still be contextual on the variants you input into the pipeline though. You could also filter the merger to sites with low-missingness in both datasets? Or does this leave you with too few SNPs that overlap the scoring files?

Carldeboer commented 6 days ago

Okay, so I'm now trying to run it with the reference you provided and am still getting errors:

$ nextflow run pgscatalog/pgsc_calc -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

NOTE: Your local project version looks outdated - a different revision is available in the remote repository [ccfd6367d5]
Launching `https://github.com/pgscatalog/pgsc_calc` [determined_panini] DSL2 - revision: ca334fa575 [main]

------------------------------------------------------
  pgscatalog/pgsc_calc v2.0.0-beta-gca334fa
------------------------------------------------------
Core Nextflow options
  revision          : main
  runName           : determined_panini
  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-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
  ld_grch37         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
  ld_grch38         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
  ancestry_checksums: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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
executor >  local (27)
executor >  local (27)
executor >  local (28)
executor >  local (31)
[da/d91ea9] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000016 PGS002814 PGS000014 PGS002426, pgp_id:, trait_efo:]) [100%] 1 of 1 ✔
[2e/99c87c] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                                          [  0%] 0 of 1
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                                                           -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR                                                          -
[skipped  ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 20)                                     [100%] 22 of 22, stored: 22 ✔
[skipped  ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE (1)                                                       [100%] 1 of 1, stored: 1 ✔
[e2/6f0718] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 10)                            [100%] 22 of 22 ✔
[skipped  ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FILTER_VARIANTS (AFcohortHG19 GRCh37)                                      [100%] 1 of 1, stored: 1 ✔
[f4/6f602f] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF (reference)                                             [100%] 1 of 1 ✔
[d8/e7e902] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_THINNED (AFcohortHG19)                                           [100%] 1 of 1 ✔
[51/52c107] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS (AFcohortHG19 null pvar)                                       [100%] 1 of 1 ✔
[3a/6e0db1] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_TARGET (AFcohortHG19)                                       [100%] 1 of 1 ✔
[1e/80bff6] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_ORIENT (AFcohortHG19)                                               [  0%] 0 of 1 ✔
[a6/03ffaf] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA (reference)                                                    [100%] 1 of 1 ✔
[-        ] 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                                                              -
[8c/9998e1] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ (AFcohortHG19 null afreq)                                         [  0%] 0 of 1
[-        ] 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                                                                        -
ERROR ~ ERROR: Projection subworkflow failed

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

And the log

$ cat .nextflow.log
Jun-24 13:42:09.726 [main] DEBUG nextflow.cli.Launcher - $> nextflow run pgscatalog/pgsc_calc -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
Jun-24 13:42:09.972 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.04.2
Jun-24 13:42:10.041 [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-pipelines2/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
Jun-24 13:42:10.069 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-24 13:42:10.071 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-24 13:42:10.076 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Jun-24 13:42:10.107 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jun-24 13:42:10.166 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/scm
Jun-24 13:42:11.644 [main] DEBUG nextflow.scm.AssetManager - Git config: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/.git/config; branch: main; remote: origin; url: https://github.com/PGScatalog/pgsc_calc.git
Jun-24 13:42:11.699 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jun-24 13:42:11.723 [main] DEBUG nextflow.scm.AssetManager - Git config: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/.git/config; branch: main; remote: origin; url: https://github.com/PGScatalog/pgsc_calc.git
Jun-24 13:42:13.131 [main] INFO  nextflow.scm.AssetManager - NOTE: Your local project version looks outdated - a different revision is available in the remote repository [ccfd6367d5]
Jun-24 13:42:13.145 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/nextflow.config
Jun-24 13:42:13.148 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/nextflow.config
Jun-24 13:42:13.159 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/secrets/store.json
Jun-24 13:42:13.163 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@4966bab1] - activable => nextflow.secret.LocalSecretsProvider@4966bab1
Jun-24 13:42:13.180 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `apptainer`
Jun-24 13:42:14.225 [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]
Jun-24 13:42:14.297 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jun-24 13:42:14.299 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/pgscatalog/pgsc_calc` [determined_panini] DSL2 - revision: ca334fa575 [main]
Jun-24 13:42:14.302 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.0.0, nf-prov@1.2.2]
Jun-24 13:42:14.303 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-24 13:42:14.303 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.0.0, nf-prov@1.2.2]
Jun-24 13:42:14.304 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.0.0
Jun-24 13:42:14.345 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.0.0' resolved
Jun-24 13:42:14.346 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.0.0'
Jun-24 13:42:14.419 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.0.0
Jun-24 13:42:14.420 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-prov version: 1.2.2
Jun-24 13:42:14.447 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-prov@1.2.2' resolved
Jun-24 13:42:14.447 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-prov@1.2.2'
Jun-24 13:42:14.455 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-prov@1.2.2
Jun-24 13:42:14.632 [main] DEBUG nextflow.Session - Session UUID: 33ad8681-168d-4a94-aa08-a70eb3c04063
Jun-24 13:42:14.633 [main] DEBUG nextflow.Session - Run name: determined_panini
Jun-24 13:42:14.634 [main] DEBUG nextflow.Session - Executor pool size: 16
Jun-24 13:42:14.661 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jun-24 13:42:14.670 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-24 13:42:14.758 [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 3.10.0-1160.108.1.el7.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: 134946@login02 [206.12.119.244]
  CPUs: 16 - Mem: 187.5 GB (867.6 MB) - Swap: 0 (0)
Jun-24 13:42:14.814 [main] DEBUG nextflow.Session - Work-dir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work [nfs]
Jun-24 13:42:14.815 [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-pipelines2/assets/pgscatalog/pgsc_calc/bin
Jun-24 13:42:14.867 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-24 13:42:14.884 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-24 13:42:14.913 [main] DEBUG nextflow.Session - Observer factory: ProvObserverFactory
Jun-24 13:42:15.142 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-24 13:42:15.202 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 17; maxThreads: 1000
Jun-24 13:42:15.435 [main] DEBUG nextflow.Session - Session start
Jun-24 13:42:15.438 [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_2024-06-24_13-42-14.txt
Jun-24 13:42:15.455 [main] DEBUG nextflow.Session - Using default localLib path: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/lib
Jun-24 13:42:15.463 [main] DEBUG nextflow.Session - Adding to the classpath library: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/lib
Jun-24 13:42:16.125 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-24 13:42:16.150 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema
Jun-24 13:42:17.139 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters, paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
Jun-24 13:42:17.293 [main] INFO  nextflow.Nextflow -

------------------------------------------------------
  pgscatalog/pgsc_calc v2.0.0-beta-gca334fa
------------------------------------------------------
Core Nextflow options
  revision          : main
  runName           : determined_panini
  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-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
  ld_grch37         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
  ld_grch38         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
  ancestry_checksums: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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

Jun-24 13:42:25.743 [main] INFO  nextflow.Nextflow - Reference database provided: skipping bootstrap
Jun-24 13:42:25.859 [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
Jun-24 13:42:25.863 [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
Jun-24 13:42:25.890 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:25.890 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:25.904 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jun-24 13:42:25.916 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=16; memory=187.5 GB; capacity=16; pollInterval=100ms; dumpInterval=5m
Jun-24 13:42:25.922 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jun-24 13:42:26.179 [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
Jun-24 13:42:26.180 [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
Jun-24 13:42:26.181 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COMBINE_SCOREFILES` matches process PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES
Jun-24 13:42:26.184 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.184 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.285 [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
Jun-24 13:42:26.286 [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
Jun-24 13:42:26.288 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_RELABELBIM` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM
Jun-24 13:42:26.298 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.299 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.335 [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
Jun-24 13:42:26.336 [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
Jun-24 13:42:26.336 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_RELABELPVAR` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR
Jun-24 13:42:26.340 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.340 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.370 [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
Jun-24 13:42:26.371 [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
Jun-24 13:42:26.372 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_VCF` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF
Jun-24 13:42:26.376 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.376 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.461 [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
Jun-24 13:42:26.462 [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
Jun-24 13:42:26.466 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.467 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.548 [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
Jun-24 13:42:26.548 [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
Jun-24 13:42:26.551 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.551 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.627 [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
Jun-24 13:42:26.628 [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
Jun-24 13:42:26.632 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.632 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.665 [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
Jun-24 13:42:26.667 [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
Jun-24 13:42:26.671 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.671 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.709 [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
Jun-24 13:42:26.709 [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
Jun-24 13:42:26.710 [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
Jun-24 13:42:26.712 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.713 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.730 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS
Jun-24 13:42:26.731 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS
Jun-24 13:42:26.733 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.733 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.758 [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_TARGET
Jun-24 13:42:26.759 [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_TARGET
Jun-24 13:42:26.762 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.762 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.792 [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_ORIENT
Jun-24 13:42:26.793 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_ORIENT
Jun-24 13:42:26.796 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.797 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.826 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,fraposa` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA
Jun-24 13:42:26.827 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:fraposa` matches labels `process_high_memory,fraposa` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA
Jun-24 13:42:26.829 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.829 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.858 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,fraposa` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT
Jun-24 13:42:26.858 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:fraposa` matches labels `process_high_memory,fraposa` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT
Jun-24 13:42:26.861 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.862 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.912 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-24 13:42:26.913 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-24 13:42:26.914 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MATCH_VARIANTS|MATCH_COMBINE` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-24 13:42:26.918 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.918 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:26.964 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-24 13:42:26.965 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-24 13:42:26.970 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MATCH_VARIANTS|MATCH_COMBINE` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-24 13:42:26.972 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:26.972 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:27.053 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_SCOREFILES
Jun-24 13:42:27.053 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_SCOREFILES
Jun-24 13:42:27.056 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:27.056 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:27.088 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ
Jun-24 13:42:27.089 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ
Jun-24 13:42:27.092 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:27.092 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:27.123 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-24 13:42:27.123 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-24 13:42:27.124 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-24 13:42:27.124 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-24 13:42:27.125 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_SCORE` matches process PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-24 13:42:27.127 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:27.127 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:27.163 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE
Jun-24 13:42:27.164 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_high_memory,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE
Jun-24 13:42:27.166 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:27.166 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:27.224 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:ANCESTRY_ANALYSIS
Jun-24 13:42:27.225 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_low,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:ANCESTRY_ANALYSIS
Jun-24 13:42:27.227 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:27.229 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:27.277 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,report` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-24 13:42:27.277 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:report` matches labels `process_high_memory,report` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-24 13:42:27.278 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PGSCATALOG_GET|SCORE_REPORT` matches process PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-24 13:42:27.280 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:27.280 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:27.335 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pyyaml` matches labels `pyyaml` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS
Jun-24 13:42:27.335 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DUMPSOFTWAREVERSIONS` matches process PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS
Jun-24 13:42:27.337 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-24 13:42:27.338 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-24 13:42:27.343 [main] DEBUG nextflow.Session - Config process names validation disabled as requested
Jun-24 13:42:27.345 [main] DEBUG nextflow.Session - Igniting dataflow network (51)
Jun-24 13:42:27.357 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES
Jun-24 13:42:27.358 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES
Jun-24 13:42:27.359 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM
Jun-24 13:42:27.361 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR
Jun-24 13:42:27.361 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF
Jun-24 13:42:27.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE
Jun-24 13:42:27.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS
Jun-24 13:42:27.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FILTER_VARIANTS
Jun-24 13:42:27.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF
Jun-24 13:42:27.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_THINNED
Jun-24 13:42:27.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS
Jun-24 13:42:27.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_TARGET
Jun-24 13:42:27.366 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_ORIENT
Jun-24 13:42:27.366 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA
Jun-24 13:42:27.366 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT
Jun-24 13:42:27.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-24 13:42:27.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-24 13:42:27.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_SCOREFILES
Jun-24 13:42:27.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ
Jun-24 13:42:27.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-24 13:42:27.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE
Jun-24 13:42:27.372 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:ANCESTRY_ANALYSIS
Jun-24 13:42:27.373 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-24 13:42:27.373 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS
Jun-24 13:42:27.375 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_6959f3d68143b55a: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/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-pipelines2/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-pipelines2/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-pipelines2/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-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/score_aggregate.nf
  Script_951dc19390c5c741: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/combine_scorefiles.nf
  Script_1317eccf6cefc502: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/ancestry_project.nf
  Script_12c9a6a07f86b4fa: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../modules/local/download_scorefiles.nf
  Script_a1b2ac31471479b0: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/pgsc_calc.nf
  Script_67ef02006e15f7bf: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/bootstrap/make_database.nf
  Script_e72266e4c23a6709: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/bootstrap_ancestry.nf
  Script_85d9c5de3f9419f5: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_score.nf
  Script_49dad12165a607ad: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/main.nf
  Script_dd9e9d3067ae34d9: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_vcf.nf
  Script_7877cbba589aaba3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_relabelbim.nf
  Script_ddfebfdd3f2163fa: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/intersect_thinned.nf
  Script_e8e89f1db16463e9: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/input_check.nf
  Script_1325f56916418255: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_relabelpvar.nf
  Script_0fa47898366f4cc3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/make_compatible.nf
  Script_dac204016b7d984d: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/match_combine.nf
  Script_71125e7d812b2828: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/apply_score.nf
  Script_7471b788f1a2a9d3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/report.nf
  Script_a1be163d058c7f54: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../modules/local/dumpsoftwareversions.nf
  Script_5556e4a34f537c27: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/match.nf
  Script_b5a82ee5e9eb54e0: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/score_report.nf
  Script_7237b9b1d4f9edb3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/match_variants.nf
  Script_75119a130470a3ec: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/relabel_ids.nf
Jun-24 13:42:27.375 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jun-24 13:42:27.375 [main] DEBUG nextflow.Session - Session await
Jun-24 13:42:27.649 [Actor Thread 27] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://ghcr.io/pgscatalog/pygscatalog:pgscatalog-utils-1.1.2; path=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/singularity/ghcr.io-pgscatalog-pygscatalog-pgscatalog-utils-1.1.2.img
Jun-24 13:42:27.725 [Actor Thread 14] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE (1)
Jun-24 13:42:27.752 [Actor Thread 23] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (16)
Jun-24 13:42:27.753 [Actor Thread 8] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (3)
Jun-24 13:42:27.755 [Actor Thread 9] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (4)
Jun-24 13:42:27.759 [Actor Thread 13] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (1)
Jun-24 13:42:27.767 [Actor Thread 6] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (5)
Jun-24 13:42:27.767 [Actor Thread 1] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (10)
Jun-24 13:42:27.769 [Actor Thread 3] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (9)
Jun-24 13:42:27.773 [Actor Thread 21] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (14)
Jun-24 13:42:27.773 [Actor Thread 2] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (8)
Jun-24 13:42:27.773 [Actor Thread 20] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (13)
Jun-24 13:42:27.773 [Actor Thread 11] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (2)
Jun-24 13:42:27.774 [Actor Thread 22] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (15)
Jun-24 13:42:27.774 [Actor Thread 4] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (7)
Jun-24 13:42:27.775 [Actor Thread 5] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (6)
Jun-24 13:42:27.776 [Actor Thread 19] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (12)
Jun-24 13:42:27.777 [Actor Thread 18] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (11)
Jun-24 13:42:27.884 [Actor Thread 4] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (18)
Jun-24 13:42:27.891 [Actor Thread 35] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (22)
Jun-24 13:42:27.895 [Actor Thread 31] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (17)
Jun-24 13:42:27.895 [Actor Thread 2] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (19)
Jun-24 13:42:27.897 [Actor Thread 21] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (21)
Jun-24 13:42:27.901 [Actor Thread 22] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (20)
Jun-24 13:42:27.963 [Actor Thread 14] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE > Skipping output binding because one or more optional files are missing: fileoutparam<0:3>
Jun-24 13:42:27.963 [Actor Thread 14] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jun-24 13:42:27.994 [Actor Thread 17] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (5)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_14_matched.txt.gz` (pattern: `AFcohortHG19_14_matched.txt.gz`)
Jun-24 13:42:28.003 [Actor Thread 30] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (4)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_6_matched.txt.gz` (pattern: `AFcohortHG19_6_matched.txt.gz`)
Jun-24 13:42:28.005 [Actor Thread 35] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (3)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_12_matched.txt.gz` (pattern: `AFcohortHG19_12_matched.txt.gz`)
Jun-24 13:42:28.006 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (7)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_7_matched.txt.gz` (pattern: `AFcohortHG19_7_matched.txt.gz`)
Jun-24 13:42:28.007 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (16)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_16_matched.txt.gz` (pattern: `AFcohortHG19_16_matched.txt.gz`)
Jun-24 13:42:28.007 [Actor Thread 14] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (2)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_11_matched.txt.gz` (pattern: `AFcohortHG19_11_matched.txt.gz`)
Jun-24 13:42:28.008 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (6)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_8_matched.txt.gz` (pattern: `AFcohortHG19_8_matched.txt.gz`)
Jun-24 13:42:28.013 [Actor Thread 19] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (15)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_4_matched.txt.gz` (pattern: `AFcohortHG19_4_matched.txt.gz`)
Jun-24 13:42:28.014 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (10)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_13_matched.txt.gz` (pattern: `AFcohortHG19_13_matched.txt.gz`)
Jun-24 13:42:28.015 [Actor Thread 16] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (13)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_5_matched.txt.gz` (pattern: `AFcohortHG19_5_matched.txt.gz`)
Jun-24 13:42:28.017 [Actor Thread 27] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (8)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_15_matched.txt.gz` (pattern: `AFcohortHG19_15_matched.txt.gz`)
Jun-24 13:42:28.018 [Actor Thread 9] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (12)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_9_matched.txt.gz` (pattern: `AFcohortHG19_9_matched.txt.gz`)
Jun-24 13:42:28.018 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (1)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_3_matched.txt.gz` (pattern: `AFcohortHG19_3_matched.txt.gz`)
Jun-24 13:42:28.022 [Actor Thread 23] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (11)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_10_matched.txt.gz` (pattern: `AFcohortHG19_10_matched.txt.gz`)
Jun-24 13:42:28.024 [Actor Thread 31] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (14)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_1_matched.txt.gz` (pattern: `AFcohortHG19_1_matched.txt.gz`)
Jun-24 13:42:28.032 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.035 [Task submitter] INFO  nextflow.Session - [da/d91ea9] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000016 PGS002814 PGS000014 PGS002426, pgp_id:, trait_efo:])
Jun-24 13:42:28.061 [Actor Thread 10] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (18)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_22_matched.txt.gz` (pattern: `AFcohortHG19_22_matched.txt.gz`)
Jun-24 13:42:28.070 [Actor Thread 4] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (9)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_2_matched.txt.gz` (pattern: `AFcohortHG19_2_matched.txt.gz`)
Jun-24 13:42:28.076 [Actor Thread 27] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (17)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_18_matched.txt.gz` (pattern: `AFcohortHG19_18_matched.txt.gz`)
Jun-24 13:42:28.077 [Actor Thread 14] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (19)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_17_matched.txt.gz` (pattern: `AFcohortHG19_17_matched.txt.gz`)
Jun-24 13:42:28.080 [Actor Thread 30] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (20)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_19_matched.txt.gz` (pattern: `AFcohortHG19_19_matched.txt.gz`)
Jun-24 13:42:28.087 [Actor Thread 16] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (21)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_20_matched.txt.gz` (pattern: `AFcohortHG19_20_matched.txt.gz`)
Jun-24 13:42:28.100 [Actor Thread 17] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (22)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/intersected/AFcohortHG19_21_matched.txt.gz` (pattern: `AFcohortHG19_21_matched.txt.gz`)
Jun-24 13:42:28.121 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.125 [Task submitter] INFO  nextflow.Session - [ec/384454] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 6)
Jun-24 13:42:28.155 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.158 [Task submitter] INFO  nextflow.Session - [4b/2754e8] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 11)
Jun-24 13:42:28.200 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.201 [Task submitter] INFO  nextflow.Session - [1d/27cc28] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 5)
Jun-24 13:42:28.243 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.244 [Task submitter] INFO  nextflow.Session - [7e/2c31c6] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 15)
Jun-24 13:42:28.312 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.312 [Task submitter] INFO  nextflow.Session - [ac/d35cf7] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 8)
Jun-24 13:42:28.340 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.341 [Task submitter] INFO  nextflow.Session - [db/0835de] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 4)
Jun-24 13:42:28.372 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.372 [Task submitter] INFO  nextflow.Session - [40/bab59d] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 14)
Jun-24 13:42:28.413 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.414 [Task submitter] INFO  nextflow.Session - [c2/d5fb9d] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 3)
Jun-24 13:42:28.470 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.471 [Task submitter] INFO  nextflow.Session - [05/a6d7e1] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 13)
Jun-24 13:42:28.525 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.526 [Task submitter] INFO  nextflow.Session - [22/029899] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 16)
Jun-24 13:42:28.579 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.580 [Task submitter] INFO  nextflow.Session - [ef/240f99] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 7)
Jun-24 13:42:28.634 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.635 [Task submitter] INFO  nextflow.Session - [8e/51b06e] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 12)
Jun-24 13:42:28.704 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.705 [Task submitter] INFO  nextflow.Session - [c4/67035a] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 2)
Jun-24 13:42:28.769 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:42:28.776 [Task submitter] INFO  nextflow.Session - [0a/373e41] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 1)
Jun-24 13:45:37.608 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000016 PGS002814 PGS000014 PGS002426, pgp_id:, trait_efo:]); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/da/d91ea9388a8eee78defd2b49e3f219]
Jun-24 13:45:37.643 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-24 13:45:38.182 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:45:38.190 [Task submitter] INFO  nextflow.Session - [d5/2a774a] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 9)
Jun-24 13:45:38.723 [Actor Thread 33] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/NO_FILE
Jun-24 13:45:38.979 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:45:38.979 [Task submitter] INFO  nextflow.Session - [c7/a7944d] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 18)
Jun-24 13:47:26.202 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 16 -- submitted tasks are shown below
~> TaskHandler[id: 28; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 6); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ec/3844547e43d724fe78525689bd42c9]
~> TaskHandler[id: 26; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 11); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/4b/2754e8637e9d6f23899d0feccffed9]
~> TaskHandler[id: 37; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 5); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/1d/27cc28bad1d069646edc1504cd5754]
~> TaskHandler[id: 32; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 15); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/7e/2c31c62dec5d838b1b9434565a363e]
~> TaskHandler[id: 30; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 8); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ac/d35cf70fb55b2e49fd27a568683656]
~> TaskHandler[id: 39; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 4); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/db/0835decd03845c6dfd774ad6241261]
~> TaskHandler[id: 29; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 14); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/40/bab59dfb49c526295759f260baf95e]
~> TaskHandler[id: 25; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 3); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/c2/d5fb9d18c9a9b6421c4e4b8d0733ae]
~> TaskHandler[id: 34; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 13); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/05/a6d7e14c5cf0aa8fec662ddc9ab2ff]
~> TaskHandler[id: 40; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 16); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/22/0298991415bc4822f0f04d085f1612]
.. remaining tasks omitted.
Jun-24 13:47:29.272 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 7 -- tasks to be submitted are shown below
~> TaskHandler[id: 42; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 22); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/e9/03a6abc8fb6a0c76763554b994fa8a]
~> TaskHandler[id: 35; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 10); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/e2/6f071800b8f2c9d2e77718963635d5]
~> TaskHandler[id: 44; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 19); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ed/ba4acb2c95f0d0be02f308ae8c3030]
~> TaskHandler[id: 45; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 20); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/7f/396fe0d95250ac10aacabf306692d0]
~> TaskHandler[id: 43; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 17); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/e6/1128b57c13d9fd534cc2f79c53e6bf]
~> TaskHandler[id: 46; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 21); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/9e/2dd8e3e874a45a9475f2d1f45376bd]
~> TaskHandler[id: 47; name: PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/2e/99c87c8c30f6e8540a3323b8e83e78]
Jun-24 13:51:37.576 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 15); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/7e/2c31c62dec5d838b1b9434565a363e]
Jun-24 13:51:37.944 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:51:37.944 [Task submitter] INFO  nextflow.Session - [e9/03a6ab] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 22)
Jun-24 13:51:51.988 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 13); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/05/a6d7e14c5cf0aa8fec662ddc9ab2ff]
Jun-24 13:51:52.087 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:51:52.088 [Task submitter] INFO  nextflow.Session - [e2/6f0718] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 10)
Jun-24 13:51:59.174 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 16); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/22/0298991415bc4822f0f04d085f1612]
Jun-24 13:51:59.276 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:51:59.277 [Task submitter] INFO  nextflow.Session - [ed/ba4acb] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 19)
Jun-24 13:52:14.529 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 14); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/40/bab59dfb49c526295759f260baf95e]
Jun-24 13:52:14.809 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:52:14.809 [Task submitter] INFO  nextflow.Session - [7f/396fe0] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 20)
Jun-24 13:52:26.086 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 16 -- submitted tasks are shown below
~> TaskHandler[id: 28; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 6); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ec/3844547e43d724fe78525689bd42c9]
~> TaskHandler[id: 26; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 11); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/4b/2754e8637e9d6f23899d0feccffed9]
~> TaskHandler[id: 37; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 5); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/1d/27cc28bad1d069646edc1504cd5754]
~> TaskHandler[id: 30; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 8); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ac/d35cf70fb55b2e49fd27a568683656]
~> TaskHandler[id: 39; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 4); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/db/0835decd03845c6dfd774ad6241261]
~> TaskHandler[id: 25; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 3); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/c2/d5fb9d18c9a9b6421c4e4b8d0733ae]
~> TaskHandler[id: 31; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 7); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ef/240f997fbd3aa2941202f446e884d2]
~> TaskHandler[id: 27; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 12); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/8e/51b06ee4b09430643074f82f003968]
~> TaskHandler[id: 33; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 2); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/c4/67035a46c3e2aa02d6ec6952939a17]
~> TaskHandler[id: 38; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 1); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/0a/373e414f3fcc63583cdcbb5c5d1569]
.. remaining tasks omitted.
Jun-24 13:52:29.847 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 3 -- tasks to be submitted are shown below
~> TaskHandler[id: 43; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 17); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/e6/1128b57c13d9fd534cc2f79c53e6bf]
~> TaskHandler[id: 46; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 21); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/9e/2dd8e3e874a45a9475f2d1f45376bd]
~> TaskHandler[id: 47; name: PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/2e/99c87c8c30f6e8540a3323b8e83e78]
Jun-24 13:53:22.285 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 12); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/8e/51b06ee4b09430643074f82f003968]
Jun-24 13:53:22.345 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:53:22.346 [Task submitter] INFO  nextflow.Session - [e6/1128b5] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 17)
Jun-24 13:53:34.827 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 11); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/4b/2754e8637e9d6f23899d0feccffed9]
Jun-24 13:53:35.006 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:53:35.007 [Task submitter] INFO  nextflow.Session - [9e/2dd8e3] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 21)
Jun-24 13:54:01.571 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 8); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ac/d35cf70fb55b2e49fd27a568683656]
Jun-24 13:54:22.125 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 7); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ef/240f997fbd3aa2941202f446e884d2]
Jun-24 13:54:22.157 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:54:22.158 [Task submitter] INFO  nextflow.Session - [2e/99c87c] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)
Jun-24 13:54:54.059 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 6); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ec/3844547e43d724fe78525689bd42c9]
Jun-24 13:54:57.060 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 18); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/c7/a7944d3f03f75e405e7ba25621138f]
Jun-24 13:55:07.418 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 37; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 5); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/1d/27cc28bad1d069646edc1504cd5754]
Jun-24 13:55:23.518 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 4); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/db/0835decd03845c6dfd774ad6241261]
Jun-24 13:55:33.048 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 3); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/c2/d5fb9d18c9a9b6421c4e4b8d0733ae]
Jun-24 13:55:49.961 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 9); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/d5/2a774af66995e4537fdd4afa577250]
Jun-24 13:55:55.333 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 1); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/0a/373e414f3fcc63583cdcbb5c5d1569]
Jun-24 13:56:15.777 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 2); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/c4/67035a46c3e2aa02d6ec6952939a17]
Jun-24 13:56:42.958 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 42; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 22); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/e9/03a6abc8fb6a0c76763554b994fa8a]
Jun-24 13:57:26.095 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- submitted tasks are shown below
~> TaskHandler[id: 35; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 10); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/e2/6f071800b8f2c9d2e77718963635d5]
~> TaskHandler[id: 44; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 19); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ed/ba4acb2c95f0d0be02f308ae8c3030]
~> TaskHandler[id: 45; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 20); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/7f/396fe0d95250ac10aacabf306692d0]
~> TaskHandler[id: 43; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 17); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/e6/1128b57c13d9fd534cc2f79c53e6bf]
~> TaskHandler[id: 46; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 21); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/9e/2dd8e3e874a45a9475f2d1f45376bd]
~> TaskHandler[id: 47; name: PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/2e/99c87c8c30f6e8540a3323b8e83e78]
Jun-24 13:57:37.845 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 44; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 19); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ed/ba4acb2c95f0d0be02f308ae8c3030]
Jun-24 13:57:43.394 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 45; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 20); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/7f/396fe0d95250ac10aacabf306692d0]
Jun-24 13:58:13.255 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 46; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 21); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/9e/2dd8e3e874a45a9475f2d1f45376bd]
Jun-24 13:58:51.617 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 43; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 17); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/e6/1128b57c13d9fd534cc2f79c53e6bf]
Jun-24 13:59:11.672 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 10); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/e2/6f071800b8f2c9d2e77718963635d5]
Jun-24 13:59:11.755 [Actor Thread 34] INFO  nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FILTER_VARIANTS (1)
Jun-24 13:59:11.793 [Actor Thread 18] 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
Jun-24 13:59:11.832 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:59:11.832 [Task submitter] INFO  nextflow.Session - [8c/9998e1] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ (AFcohortHG19 null afreq)
Jun-24 13:59:11.887 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:59:11.887 [Task submitter] INFO  nextflow.Session - [f4/6f602f] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF (reference)
Jun-24 13:59:11.934 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:59:11.935 [Task submitter] INFO  nextflow.Session - [d8/e7e902] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_THINNED (AFcohortHG19)
Jun-24 13:59:15.536 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 51; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF (reference); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/f4/6f602fd00e3c3beec8e67d7a745b99]
Jun-24 13:59:15.553 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jun-24 13:59:15.611 [Actor Thread 10] 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
Jun-24 13:59:15.616 [Actor Thread 10] INFO  nextflow.container.SingularityCache - Pulling Apptainer image docker://ghcr.io/pgscatalog/fraposa_pgsc:v0.1.1 [cache /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/singularity/ghcr.io-pgscatalog-fraposa_pgsc-v0.1.1.img]
Jun-24 13:59:46.068 [Actor Thread 10] DEBUG nextflow.container.SingularityCache - Apptainer pull complete image=docker://ghcr.io/pgscatalog/fraposa_pgsc:v0.1.1 path=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/singularity/ghcr.io-pgscatalog-fraposa_pgsc-v0.1.1.img
Jun-24 13:59:46.165 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 13:59:46.165 [Task submitter] INFO  nextflow.Session - [a6/03ffaf] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA (reference)
Jun-24 14:00:14.463 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 52; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA (reference); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/a6/03ffaf5f4d45b43d03260f96b0b2b1]
Jun-24 14:01:16.227 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 50; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_THINNED (AFcohortHG19); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/d8/e7e90208603deee5e1796164cfd3e8]
Jun-24 14:01:16.274 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 14:01:16.275 [Task submitter] INFO  nextflow.Session - [51/52c107] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS (AFcohortHG19 null pvar)
Jun-24 14:01:21.207 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 53; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS (AFcohortHG19 null pvar); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/51/52c1070cfe8ae2d4522c1f62a9307a]
Jun-24 14:01:21.272 [Actor Thread 16] DEBUG nextflow.processor.TaskProcessor - Process `PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_TARGET (1)` is unable to find [UnixPath]: `/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ancestry/bed/GRCh37_AFcohortHG19.bed` (pattern: `GRCh37_AFcohortHG19.bed`)
Jun-24 14:01:21.321 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 14:01:21.321 [Task submitter] INFO  nextflow.Session - [3a/6e0db1] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_TARGET (AFcohortHG19)
Jun-24 14:01:22.426 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 54; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_TARGET (AFcohortHG19); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/3a/6e0db1ba44db646e933c488725564f]
Jun-24 14:01:22.448 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_TARGET > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jun-24 14:01:22.578 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-24 14:01:22.579 [Task submitter] INFO  nextflow.Session - [1e/80bff6] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_ORIENT (AFcohortHG19)
Jun-24 14:01:23.767 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 55; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_ORIENT (AFcohortHG19); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/1e/80bff6fc6af3ac5ac10245b8e022ea]
Jun-24 14:01:23.777 [Actor Thread 14] ERROR nextflow.Nextflow - ERROR: Projection subworkflow failed
nebfield commented 6 days ago

Sorry, I can't tell what's precisely going wrong from these logs. A few suggestions to try:

Carldeboer commented 5 days ago

1) deleted work/. running now. 2) We don't have docker on our HPC. Why is apptainer not pulling the singularity profiles? 3) it is local. Our jobs cannot access the internet, so submitting jobs was causing issues when nextflow was trying to download things. In the past I have tried caching the files and then submitting the jobs, but so far not gotten that far here.

Carldeboer commented 5 days ago

different error after deleting work/. I have noticed issues when some files have chromosome IDs with "chr" and some don't. If my cohort and the reference don't have the same, could that cause this? If so, what format are the chromosome IDs in the reference? The current error:

$ nextflow run pgscatalog/pgsc_calc -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

NOTE: Your local project version looks outdated - a different revision is available in the remote repository [ccfd6367d5]
Launching `https://github.com/pgscatalog/pgsc_calc` [compassionate_bardeen] DSL2 - revision: ca334fa575 [main]

------------------------------------------------------
  pgscatalog/pgsc_calc v2.0.0-beta-gca334fa
------------------------------------------------------
Core Nextflow options
  revision          : main
  runName           : compassionate_bardeen
  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-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
  ld_grch37         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
  ld_grch38         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
  ancestry_checksums: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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         -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM      -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                    -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES         -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM      -
executor >  local (7)
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                                     -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES                          -
executor >  local (8)
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                                     -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES                          -
executor >  local (8)
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                                     -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES                          -
executor >  local (8)
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                                     [  0%] 0 of 1
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES                          -
executor >  local (9)
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                                     [  0%] 0 of 1
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES                          -
executor >  local (9)
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                                     [  0%] 0 of 1
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES                          -
executor >  local (10)
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                                     [  0%] 0 of 1
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES                          -
executor >  local (11)
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                                     [  0%] 0 of 1
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES                          -
executor >  local (11)
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES                                     [  0%] 0 of 1
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES                          -
executor >  local (55)
[52/c540f5] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000016 PGS002814 PGS000014 PGS002426, pgp_id:, trait_efo:]) [100%] 1 of 1 ✔
[0c/b03f09] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                                          [100%] 1 of 1 ✔
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                                                           -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR                                                          -
[86/1c0c45] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 1)                                      [100%] 22 of 22 ✔
[2a/583314] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE (1)                                                       [100%] 1 of 1 ✔
[ea/6a9eb0] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 6)                             [ 90%] 20 of 22
[-        ] 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                                                            -
[88/53f005] process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 21)                                           [  0%] 0 of 22
[-        ] 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                                                                        -
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)'

Caused by:
  Process `PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)` terminated with an error exit status (1)

Command executed:

  export POLARS_MAX_THREADS=2

  pgscatalog-match                  --dataset AFcohortHG19         --scorefile scorefiles.txt.gz         --target GRCh37_AFcohortHG19_16.pvar.zst         --only_match         --chrom 16                           --executor >  local (55)
[52/c540f5] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000016 PGS002814 PGS000014 PGS002426, pgp_id:, trait_efo:]) [100%] 1 of 1 ✔
[0c/b03f09] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                                          [100%] 1 of 1 ✔
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                                                           -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR                                                          -
[86/1c0c45] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 1)                                      [100%] 22 of 22 ✔
[2a/583314] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE (1)                                                       [100%] 1 of 1 ✔
[ea/6a9eb0] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 6)                             [ 90%] 20 of 22
[-        ] 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                                                            -
[a5/4f69f3] process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)                                           [  4%] 1 of 22, failed: 1
[-        ] 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                                                                        -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)'

Caused by:
  Process `PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)` terminated with an error exit status (1)

Command executed:

  export POLARS_MAX_THREADS=2

  pgscatalog-match                  --dataset AFcohortHG19         --scorefile scorefiles.txt.gz         --target GRCh37_AFcohortHG19_16.pvar.zst         --only_match         --chrom 16                           --outdir $PWD         -v

  cat <<-END_VERSIONS > versions.yml
executor >  local (55)
[52/c540f5] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000016 PGS002814 PGS000014 PGS002426, pgp_id:, trait_efo:]) [100%] 1 of 1 ✔
[0c/b03f09] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                                          [100%] 1 of 1 ✔
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                                                           -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR                                                          -
[86/1c0c45] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 1)                                      [100%] 22 of 22 ✔
[2a/583314] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE (1)                                                       [100%] 1 of 1 ✔
[ea/6a9eb0] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 6)                             [ 90%] 20 of 22
[-        ] 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                                                            -
[a5/4f69f3] process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)                                           [  4%] 1 of 22, failed: 1
[-        ] 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                                                                        -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)'

Caused by:
  Process `PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)` terminated with an error exit status (1)

Command executed:

  export POLARS_MAX_THREADS=2

  pgscatalog-match                  --dataset AFcohortHG19         --scorefile scorefiles.txt.gz         --target GRCh37_AFcohortHG19_16.pvar.zst         --only_match         --chrom 16                           --outdir $PWD         -v

  cat <<-END_VERSIONS > versions.yml
  MATCH_VARIANTS:
      pgscatalog.match: $(echo $(python -c 'import pgscatalog.match; print(pgscatalog.match.__version__)'))
  END_VERSIONS
executor >  local (55)
[52/c540f5] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000016 PGS002814 PGS000014 PGS002426, pgp_id:, trait_efo:]) [100%] 1 of 1 ✔
[0c/b03f09] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                                          [100%] 1 of 1 ✔
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                                                           -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR                                                          -
[86/1c0c45] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 1)                                      [100%] 22 of 22 ✔
[2a/583314] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE (1)                                                       [100%] 1 of 1 ✔
[ea/6a9eb0] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 6)                             [ 90%] 20 of 22
[-        ] 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                                                            -
[a5/4f69f3] process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)                                           [  4%] 1 of 22, failed: 1
[-        ] 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                                                                        -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)'

Caused by:
  Process `PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)` terminated with an error exit status (1)

Command executed:

  export POLARS_MAX_THREADS=2

  pgscatalog-match                  --dataset AFcohortHG19         --scorefile scorefiles.txt.gz         --target GRCh37_AFcohortHG19_16.pvar.zst         --only_match         --chrom 16                           --outdir $PWD         -v

  cat <<-END_VERSIONS > versions.yml
  MATCH_VARIANTS:
      pgscatalog.match: $(echo $(python -c 'import pgscatalog.match; print(pgscatalog.match.__version__)'))
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  pgscatalog.match.cli.match_cli: 2024-06-25 08:52:43 WARNING  No output format specified, writing to combined scoring file
  pgscatalog.match.cli.match_cli: 2024-06-25 08:52:43 DEBUG    Verbose logging enabled
  pgscatalog.match.cli.match_cli: 2024-06-25 08:52:43 INFO     --cleanup set (default), temporary files will be deleted
  pgscatalog.match.lib.scoringfileframe: 2024-06-25 08:52:43 DEBUG    Converting ScoringFileFrame(NormalisedScoringFile('scorefiles.txt.gz')) to feather format
  pgscatalog.match.lib.scoringfileframe: 2024-06-25 08:52:54 DEBUG    ScoringFileFrame(NormalisedScoringFile('scorefiles.txt.gz')) feather conversion complete
  pgscatalog.match.lib._match.preprocess: 2024-06-25 08:52:55 DEBUG    Complementing column effect_allele
  pgscatalog.match.lib._match.preprocess: 2024-06-25 08:52:55 DEBUG    Complementing column other_allele
  pgscatalog.match.lib.scoringfileframe: 2024-06-25 08:52:55 DEBUG    Filtering scoring file to chromosome 16
  pgscatalog.match.lib.variantframe: 2024-06-25 08:52:55 DEBUG    Converting VariantFrame(path='GRCh37_AFcohortHG19_16.pvar.zst', dataset='AFcohortHG19', chrom='16', cleanup=True, tmpdir=PosixPath('tmp')) to feather format
  Traceback (most recent call last):
    File "/app/pgscatalog.utils/.venv/bin/pgscatalog-match", line 8, in <module>
      sys.exit(run_match())
               ^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/cli/match_cli.py", line 87, in run_match
      ipc_path = get_match_candidates(
                 ^^^^^^^^^^^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/cli/match_cli.py", line 124, in get_match_candidates
      with variants as target_df:
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/lib/variantframe.py", line 54, in __enter__
      self.arrowpaths = loose(self.variants, tmpdir=self._tmpdir)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/functools.py", line 909, in wrapper
      return dispatch(args[0].__class__)(*args, **kw)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/lib/_arrow.py", line 94, in _
      return batch_read(reader, tmpdir=tmpdir, cols_keep=cols_keep)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/lib/_arrow.py", line 102, in batch_read
      batches = reader.next_batches(batch_size)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/polars/io/csv/batched_reader.py", line 134, in next_batches
      batches = self._reader.next_batches(n)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  polars.exceptions.ComputeError: found more fields than defined in 'Schema'

  Consider setting 'truncate_ragged_lines=True'.
  Exception ignored in atexit callback: <function _exit at 0x2aaaab5580e0>
  Traceback (most recent call last):
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/cli/match_cli.py", line 31, in _exit
      shutil.rmtree(Config.MATCHTMP)
    File "/usr/local/lib/python3.11/shutil.py", line 763, in rmtree
      onerror(os.rmdir, path, sys.exc_info())
    File "/usr/local/lib/python3.11/shutil.py", line 761, in rmtree
      os.rmdir(path, dir_fd=dir_fd)
  OSError: [Errno 39] Directory not empty: 'matchtmp'

Work dir:
  /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/a5/4f69f378e510ce2001d4bd1262724d

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

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

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

 -- Check '.nextflow.log' file for details
ERROR ~ ERROR: No scores calculated!

 -- Check '.nextflow.log' file for details
ERROR ~ ERROR: No results report written!

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

and the log

$ cat .nextflow.log
Jun-25 08:36:29.253 [main] DEBUG nextflow.cli.Launcher - $> nextflow run pgscatalog/pgsc_calc -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
Jun-25 08:36:29.484 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.04.2
Jun-25 08:36:29.539 [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-pipelines2/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
Jun-25 08:36:29.565 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-25 08:36:29.568 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-25 08:36:29.573 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Jun-25 08:36:29.594 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jun-25 08:36:29.641 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/scm
Jun-25 08:36:30.977 [main] DEBUG nextflow.scm.AssetManager - Git config: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/.git/config; branch: main; remote: origin; url: https://github.com/PGScatalog/pgsc_calc.git
Jun-25 08:36:31.023 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jun-25 08:36:31.044 [main] DEBUG nextflow.scm.AssetManager - Git config: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/.git/config; branch: main; remote: origin; url: https://github.com/PGScatalog/pgsc_calc.git
Jun-25 08:36:32.243 [main] INFO  nextflow.scm.AssetManager - NOTE: Your local project version looks outdated - a different revision is available in the remote repository [ccfd6367d5]
Jun-25 08:36:32.256 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/nextflow.config
Jun-25 08:36:32.259 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/nextflow.config
Jun-25 08:36:32.268 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/secrets/store.json
Jun-25 08:36:32.272 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@2bebd114] - activable => nextflow.secret.LocalSecretsProvider@2bebd114
Jun-25 08:36:32.287 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `apptainer`
Jun-25 08:36:33.140 [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]
Jun-25 08:36:33.198 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jun-25 08:36:33.199 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/pgscatalog/pgsc_calc` [compassionate_bardeen] DSL2 - revision: ca334fa575 [main]
Jun-25 08:36:33.201 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.0.0, nf-prov@1.2.2]
Jun-25 08:36:33.202 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-25 08:36:33.202 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.0.0, nf-prov@1.2.2]
Jun-25 08:36:33.203 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.0.0
Jun-25 08:36:33.237 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.0.0' resolved
Jun-25 08:36:33.237 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.0.0'
Jun-25 08:36:33.263 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.0.0
Jun-25 08:36:33.264 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-prov version: 1.2.2
Jun-25 08:36:33.285 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-prov@1.2.2' resolved
Jun-25 08:36:33.285 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-prov@1.2.2'
Jun-25 08:36:33.292 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-prov@1.2.2
Jun-25 08:36:33.405 [main] DEBUG nextflow.Session - Session UUID: 840d47e6-835f-4d22-999d-922b5241ed38
Jun-25 08:36:33.405 [main] DEBUG nextflow.Session - Run name: compassionate_bardeen
Jun-25 08:36:33.406 [main] DEBUG nextflow.Session - Executor pool size: 16
Jun-25 08:36:33.421 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jun-25 08:36:33.432 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-25 08:36:33.475 [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 3.10.0-1160.108.1.el7.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: 121218@login02 [206.12.119.244]
  CPUs: 16 - Mem: 187.5 GB (8.3 GB) - Swap: 0 (0)
Jun-25 08:36:33.525 [main] DEBUG nextflow.Session - Work-dir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work [nfs]
Jun-25 08:36:33.526 [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-pipelines2/assets/pgscatalog/pgsc_calc/bin
Jun-25 08:36:33.570 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-25 08:36:33.589 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-25 08:36:33.618 [main] DEBUG nextflow.Session - Observer factory: ProvObserverFactory
Jun-25 08:36:33.795 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-25 08:36:33.817 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 17; maxThreads: 1000
Jun-25 08:36:34.029 [main] DEBUG nextflow.Session - Session start
Jun-25 08:36:34.031 [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_2024-06-25_08-36-32.txt
Jun-25 08:36:34.044 [main] DEBUG nextflow.Session - Using default localLib path: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/lib
Jun-25 08:36:34.051 [main] DEBUG nextflow.Session - Adding to the classpath library: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/lib
Jun-25 08:36:34.652 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-25 08:36:34.669 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema
Jun-25 08:36:35.492 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters, paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
Jun-25 08:36:35.592 [main] INFO  nextflow.Nextflow -

------------------------------------------------------
  pgscatalog/pgsc_calc v2.0.0-beta-gca334fa
------------------------------------------------------
Core Nextflow options
  revision          : main
  runName           : compassionate_bardeen
  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-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
  ld_grch37         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
  ld_grch38         : /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
  ancestry_checksums: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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

Jun-25 08:36:41.236 [main] INFO  nextflow.Nextflow - Reference database provided: skipping bootstrap
Jun-25 08:36:41.334 [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
Jun-25 08:36:41.336 [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
Jun-25 08:36:41.352 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:41.352 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:41.361 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jun-25 08:36:41.370 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=16; memory=187.5 GB; capacity=16; pollInterval=100ms; dumpInterval=5m
Jun-25 08:36:41.375 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jun-25 08:36:41.575 [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
Jun-25 08:36:41.576 [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
Jun-25 08:36:41.576 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COMBINE_SCOREFILES` matches process PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES
Jun-25 08:36:41.579 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:41.579 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:41.660 [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
Jun-25 08:36:41.661 [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
Jun-25 08:36:41.663 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_RELABELBIM` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM
Jun-25 08:36:41.671 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:41.671 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:41.701 [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
Jun-25 08:36:41.702 [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
Jun-25 08:36:41.702 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_RELABELPVAR` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR
Jun-25 08:36:41.708 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:41.708 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:41.731 [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
Jun-25 08:36:41.732 [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
Jun-25 08:36:41.733 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_VCF` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF
Jun-25 08:36:41.737 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:41.737 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:41.803 [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
Jun-25 08:36:41.804 [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
Jun-25 08:36:41.807 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:41.807 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:41.868 [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
Jun-25 08:36:41.869 [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
Jun-25 08:36:41.872 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:41.872 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:41.917 [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
Jun-25 08:36:41.918 [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
Jun-25 08:36:41.922 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:41.922 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:41.949 [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
Jun-25 08:36:41.951 [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
Jun-25 08:36:41.955 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:41.955 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:41.989 [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
Jun-25 08:36:41.989 [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
Jun-25 08:36:41.990 [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
Jun-25 08:36:41.992 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:41.992 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.008 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS
Jun-25 08:36:42.009 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS
Jun-25 08:36:42.011 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.012 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.034 [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_TARGET
Jun-25 08:36:42.035 [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_TARGET
Jun-25 08:36:42.038 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.038 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.065 [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_ORIENT
Jun-25 08:36:42.066 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_ORIENT
Jun-25 08:36:42.069 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.070 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.097 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,fraposa` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA
Jun-25 08:36:42.098 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:fraposa` matches labels `process_high_memory,fraposa` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA
Jun-25 08:36:42.100 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.100 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.125 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,fraposa` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT
Jun-25 08:36:42.125 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:fraposa` matches labels `process_high_memory,fraposa` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT
Jun-25 08:36:42.128 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.128 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.175 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-25 08:36:42.175 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-25 08:36:42.176 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MATCH_VARIANTS|MATCH_COMBINE` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-25 08:36:42.180 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.180 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.218 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-25 08:36:42.219 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-25 08:36:42.220 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MATCH_VARIANTS|MATCH_COMBINE` matches process PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-25 08:36:42.222 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.222 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.277 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_SCOREFILES
Jun-25 08:36:42.277 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_SCOREFILES
Jun-25 08:36:42.280 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.280 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.307 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ
Jun-25 08:36:42.308 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ
Jun-25 08:36:42.310 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.310 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.333 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-25 08:36:42.333 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-25 08:36:42.334 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-25 08:36:42.334 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-25 08:36:42.335 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_SCORE` matches process PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-25 08:36:42.337 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.337 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.369 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE
Jun-25 08:36:42.370 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_high_memory,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE
Jun-25 08:36:42.372 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.372 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.417 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:ANCESTRY_ANALYSIS
Jun-25 08:36:42.418 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_low,pgscatalog_utils` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:ANCESTRY_ANALYSIS
Jun-25 08:36:42.420 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.420 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.456 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,report` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-25 08:36:42.457 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:report` matches labels `process_high_memory,report` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-25 08:36:42.458 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PGSCATALOG_GET|SCORE_REPORT` matches process PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-25 08:36:42.460 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.460 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pyyaml` matches labels `pyyaml` for process with name PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS
Jun-25 08:36:42.501 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DUMPSOFTWAREVERSIONS` matches process PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS
Jun-25 08:36:42.503 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 08:36:42.503 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 08:36:42.507 [main] DEBUG nextflow.Session - Config process names validation disabled as requested
Jun-25 08:36:42.509 [main] DEBUG nextflow.Session - Igniting dataflow network (51)
Jun-25 08:36:42.519 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES
Jun-25 08:36:42.520 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES
Jun-25 08:36:42.521 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM
Jun-25 08:36:42.521 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR
Jun-25 08:36:42.522 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF
Jun-25 08:36:42.524 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE
Jun-25 08:36:42.524 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS
Jun-25 08:36:42.525 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FILTER_VARIANTS
Jun-25 08:36:42.525 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF
Jun-25 08:36:42.525 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_THINNED
Jun-25 08:36:42.525 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS
Jun-25 08:36:42.525 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_TARGET
Jun-25 08:36:42.525 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_ORIENT
Jun-25 08:36:42.525 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA
Jun-25 08:36:42.525 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT
Jun-25 08:36:42.529 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-25 08:36:42.529 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-25 08:36:42.530 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_SCOREFILES
Jun-25 08:36:42.530 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ
Jun-25 08:36:42.530 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-25 08:36:42.530 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE
Jun-25 08:36:42.532 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:ANCESTRY_ANALYSIS
Jun-25 08:36:42.532 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-25 08:36:42.532 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS
Jun-25 08:36:42.534 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_6959f3d68143b55a: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/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-pipelines2/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-pipelines2/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-pipelines2/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-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/score_aggregate.nf
  Script_951dc19390c5c741: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/combine_scorefiles.nf
  Script_1317eccf6cefc502: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/ancestry_project.nf
  Script_12c9a6a07f86b4fa: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../modules/local/download_scorefiles.nf
  Script_a1b2ac31471479b0: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/pgsc_calc.nf
  Script_67ef02006e15f7bf: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_score.nf
  Script_e72266e4c23a6709: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/bootstrap_ancestry.nf
  Script_49dad12165a607ad: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/main.nf
  Script_dd9e9d3067ae34d9: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_vcf.nf
  Script_ddfebfdd3f2163fa: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/intersect_thinned.nf
  Script_7877cbba589aaba3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_relabelbim.nf
  Script_0fa47898366f4cc3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/make_compatible.nf
  Script_1325f56916418255: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_relabelpvar.nf
  Script_e8e89f1db16463e9: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/input_check.nf
  Script_dac204016b7d984d: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/match_combine.nf
  Script_71125e7d812b2828: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/apply_score.nf
  Script_7471b788f1a2a9d3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/report.nf
  Script_a1be163d058c7f54: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../modules/local/dumpsoftwareversions.nf
  Script_5556e4a34f537c27: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/match.nf
  Script_b5a82ee5e9eb54e0: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/score_report.nf
  Script_7237b9b1d4f9edb3: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/match_variants.nf
  Script_75119a130470a3ec: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/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-pipelines2/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-pipelines2/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/relabel_ids.nf
Jun-25 08:36:42.535 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jun-25 08:36:42.535 [main] DEBUG nextflow.Session - Session await
Jun-25 08:36:42.734 [Actor Thread 26] 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
Jun-25 08:36:42.737 [Actor Thread 24] 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]
Jun-25 08:36:42.737 [Actor Thread 26] INFO  nextflow.container.SingularityCache - Pulling Apptainer image docker://dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/zstd:1.4.8 [cache /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/singularity/dockerhub.ebi.ac.uk-gdp-public-pgsc_calc-zstd-1.4.8.img]
Jun-25 08:36:42.737 [Actor Thread 25] INFO  nextflow.container.SingularityCache - Pulling Apptainer image docker://ghcr.io/pgscatalog/plink2:2.00a5.10 [cache /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/singularity/ghcr.io-pgscatalog-plink2-2.00a5.10.img]
Jun-25 08:36:44.350 [Actor Thread 25] DEBUG nextflow.container.SingularityCache - Apptainer pull complete 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
Jun-25 08:36:44.548 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:36:44.551 [Task submitter] INFO  nextflow.Session - [09/6f2c1e] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 16)
Jun-25 08:36:44.572 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:36:44.573 [Task submitter] INFO  nextflow.Session - [14/26a2c9] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 8)
Jun-25 08:36:44.600 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:36:44.600 [Task submitter] INFO  nextflow.Session - [97/7d5ba9] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 4)
Jun-25 08:36:44.631 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:36:44.631 [Task submitter] INFO  nextflow.Session - [c1/db8f7a] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 7)
Jun-25 08:36:44.653 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:36:44.654 [Task submitter] INFO  nextflow.Session - [74/baebfa] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 5)
Jun-25 08:36:44.683 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:36:44.684 [Task submitter] INFO  nextflow.Session - [19/7573c2] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 10)
Jun-25 08:36:44.717 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:36:44.717 [Task submitter] INFO  nextflow.Session - [5e/be06e9] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 15)
Jun-25 08:36:44.764 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:36:44.765 [Task submitter] INFO  nextflow.Session - [d7/87e009] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 14)
Jun-25 08:36:46.512 [Actor Thread 26] DEBUG nextflow.container.SingularityCache - Apptainer pull complete 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
Jun-25 08:36:46.652 [Actor Thread 24] DEBUG nextflow.container.SingularityCache - Apptainer pull complete image=docker://ghcr.io/pgscatalog/pygscatalog:pgscatalog-utils-1.1.2 path=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/singularity/ghcr.io-pgscatalog-pygscatalog-pgscatalog-utils-1.1.2.img
Jun-25 08:37:06.187 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 15); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/5e/be06e968cf8aa6da89a04667d74b39]
Jun-25 08:37:06.189 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-25 08:37:06.205 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:06.205 [Task submitter] INFO  nextflow.Session - [73/9c47a8] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 12)
Jun-25 08:37:07.753 [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: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/d7/87e009cf6558ded6252fe6a2b06e74]
Jun-25 08:37:07.800 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:07.801 [Task submitter] INFO  nextflow.Session - [c2/ca69cc] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 3)
Jun-25 08:37:08.223 [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: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/09/6f2c1edfdf7e0786d708ef55f0baf4]
Jun-25 08:37:08.268 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:08.268 [Task submitter] INFO  nextflow.Session - [1a/8400e8] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 9)
Jun-25 08:37:18.118 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 10); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/19/7573c216f17f870ae97b505b0ac4b3]
Jun-25 08:37:18.142 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:18.142 [Task submitter] INFO  nextflow.Session - [2d/f89746] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 2)
Jun-25 08:37:22.980 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 8); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/14/26a2c968b4d6202dcc6b58e684e0f9]
Jun-25 08:37:23.014 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:23.015 [Task submitter] INFO  nextflow.Session - [2f/0ec31a] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 11)
Jun-25 08:37:24.158 [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: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/c1/db8f7a1fcf5945db9e68b221363e24]
Jun-25 08:37:24.181 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:24.182 [Task submitter] INFO  nextflow.Session - [f5/27c189] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 13)
Jun-25 08:37:27.962 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 5); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/74/baebfae0e44ed36b46397e4b45b9e9]
Jun-25 08:37:27.979 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:27.980 [Task submitter] INFO  nextflow.Session - [66/9824c5] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 6)
Jun-25 08:37:32.360 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 4); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/97/7d5ba9ef81c265f3176254d07ccfd0]
Jun-25 08:37:32.390 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:32.403 [Task submitter] INFO  nextflow.Session - [86/1c0c45] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 1)
Jun-25 08:37:36.418 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 9); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/1a/8400e8649e1f48c93657f91eb3889f]
Jun-25 08:37:36.456 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:36.457 [Task submitter] INFO  nextflow.Session - [7d/91287b] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 18)
Jun-25 08:37:36.864 [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: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/73/9c47a86608c75804fb92fd446ef84c]
Jun-25 08:37:36.887 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:36.890 [Task submitter] INFO  nextflow.Session - [1a/1d6b94] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 17)
Jun-25 08:37:46.880 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 13); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/f5/27c1896ba01b61bb088d30f6b788a1]
Jun-25 08:37:46.931 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:46.931 [Task submitter] INFO  nextflow.Session - [e9/e2ded8] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 21)
Jun-25 08:37:52.590 [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: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/c2/ca69ccb82ddc1b02ef82fd22a37b0a]
Jun-25 08:37:52.612 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:52.613 [Task submitter] INFO  nextflow.Session - [d8/5cbb34] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 22)
Jun-25 08:37:54.778 [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: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/2f/0ec31a09d674ba4f6a53b2c314f13d]
Jun-25 08:37:54.800 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:54.800 [Task submitter] INFO  nextflow.Session - [4e/caed42] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 20)
Jun-25 08:37:56.304 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 18); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/7d/91287b093b5fe3638a16e9bc2bee47]
Jun-25 08:37:56.330 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:56.331 [Task submitter] INFO  nextflow.Session - [01/811087] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 19)
Jun-25 08:37:56.736 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 17); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/1a/1d6b94aa0e7626d58dc3555460a4e8]
Jun-25 08:37:56.761 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:56.761 [Task submitter] INFO  nextflow.Session - [2a/583314] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE (1)
Jun-25 08:37:56.997 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 21); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/e9/e2ded815932f229a465883e566c80b]
Jun-25 08:37:57.015 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:37:57.015 [Task submitter] INFO  nextflow.Session - [52/c540f5] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000016 PGS002814 PGS000014 PGS002426, pgp_id:, trait_efo:])
Jun-25 08:38:02.677 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 22); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/d8/5cbb3450612f2fcc566df6045ff217]
Jun-25 08:38:07.511 [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: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/66/9824c506a780ea747c945b3409be3f]
Jun-25 08:38:09.722 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 20); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/4e/caed4210f7915d635dc25ae9f7ff04]
Jun-25 08:38:11.098 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 2); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/2d/f897460493dc11d8b9abe68feda87b]
Jun-25 08:38:11.459 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (AFcohortHG19 chromosome 19); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/01/8110873b8b2e25da743660f00f1454]
Jun-25 08:38:29.498 [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: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/86/1c0c45a89c45ddd42776ba5d215a66]
Jun-25 08:39:24.067 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE (1); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/2a/583314e0e08597d9c20d2949f18a3a]
Jun-25 08:39:24.225 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE > Skipping output binding because one or more optional files are missing: fileoutparam<0:3>
Jun-25 08:39:24.225 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jun-25 08:39:24.355 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.356 [Task submitter] INFO  nextflow.Session - [03/823f3a] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 21)
Jun-25 08:39:24.380 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.380 [Task submitter] INFO  nextflow.Session - [78/ab0335] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 17)
Jun-25 08:39:24.401 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.401 [Task submitter] INFO  nextflow.Session - [e5/f25386] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 13)
Jun-25 08:39:24.421 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.422 [Task submitter] INFO  nextflow.Session - [a4/0b6a78] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 11)
Jun-25 08:39:24.443 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.443 [Task submitter] INFO  nextflow.Session - [69/dd6826] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 7)
Jun-25 08:39:24.469 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.470 [Task submitter] INFO  nextflow.Session - [ac/70f619] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 18)
Jun-25 08:39:24.498 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.498 [Task submitter] INFO  nextflow.Session - [25/45aaf1] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 10)
Jun-25 08:39:24.527 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.527 [Task submitter] INFO  nextflow.Session - [68/1856a3] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 5)
Jun-25 08:39:24.561 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.562 [Task submitter] INFO  nextflow.Session - [06/776613] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 14)
Jun-25 08:39:24.599 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.600 [Task submitter] INFO  nextflow.Session - [15/e0ed1b] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 8)
Jun-25 08:39:24.636 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.636 [Task submitter] INFO  nextflow.Session - [a9/d21cbd] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 12)
Jun-25 08:39:24.681 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.681 [Task submitter] INFO  nextflow.Session - [17/081a9d] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 9)
Jun-25 08:39:24.725 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.726 [Task submitter] INFO  nextflow.Session - [d9/c6f95d] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 16)
Jun-25 08:39:24.769 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:39:24.769 [Task submitter] INFO  nextflow.Session - [83/3b2b8f] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 3)
Jun-25 08:40:57.869 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000016 PGS002814 PGS000014 PGS002426, pgp_id:, trait_efo:]); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/52/c540f55bc82299f139a61b3f856e22]
Jun-25 08:40:58.018 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:40:58.019 [Task submitter] INFO  nextflow.Session - [90/6758e1] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 15)
Jun-25 08:40:58.259 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:40:58.259 [Task submitter] INFO  nextflow.Session - [5a/bd2c46] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 4)
Jun-25 08:40:58.343 [Actor Thread 31] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/my-pipelines2/assets/pgscatalog/pgsc_calc/assets/NO_FILE
Jun-25 08:41:41.516 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 16 -- submitted tasks are shown below
~> TaskHandler[id: 40; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 21); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/03/823f3a87d2ba9d9bcef8217271b440]
~> TaskHandler[id: 39; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 17); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/78/ab0335f027acd1ec76521f5c9982ab]
~> TaskHandler[id: 35; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 13); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/e5/f2538646f9064deb1a68273514a5e2]
~> TaskHandler[id: 37; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 11); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/a4/0b6a783cc9382b540a63e6c7cbd209]
~> TaskHandler[id: 30; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 7); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/69/dd68266b13ab089061b127db119243]
~> TaskHandler[id: 38; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 18); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ac/70f619dad85cc11bf18c09ce595f80]
~> TaskHandler[id: 28; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 10); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/25/45aaf1b2c6b7f973a6b808778df80f]
~> TaskHandler[id: 31; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 5); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/68/1856a35a9426f3babd76c50e401e7e]
~> TaskHandler[id: 26; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 14); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/06/776613bfa69fb681a2610c6b843c68]
~> TaskHandler[id: 29; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 8); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/15/e0ed1bd375b2d38f9130febff802cb]
.. remaining tasks omitted.
Jun-25 08:41:45.427 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 7 -- tasks to be submitted are shown below
~> TaskHandler[id: 41; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 22); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/f8/4d8ddb7bd8f262e05ac63d94498b7e]
~> TaskHandler[id: 42; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 6); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ea/6a9eb08839544b942e2051413edac1]
~> TaskHandler[id: 44; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 2); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/6c/17e539546864b21046e4b232fb2488]
~> TaskHandler[id: 43; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 20); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/57/6bcd76bc811dd6d19464e2f3b51479]
~> TaskHandler[id: 45; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 19); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/18/ae935c1e4f2186619fda54ebfbfbb0]
~> TaskHandler[id: 46; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 1); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/d2/01a05786f6ed6ab26367b2ba41c65f]
~> TaskHandler[id: 47; name: PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/0c/b03f09bb5e3364ac878c79e5254c4b]
Jun-25 08:43:52.671 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 21); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/03/823f3a87d2ba9d9bcef8217271b440]
Jun-25 08:43:52.713 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:43:52.714 [Task submitter] INFO  nextflow.Session - [f8/4d8ddb] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 22)
Jun-25 08:44:53.216 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 18); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ac/70f619dad85cc11bf18c09ce595f80]
Jun-25 08:44:53.348 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:44:53.349 [Task submitter] INFO  nextflow.Session - [ea/6a9eb0] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 6)
Jun-25 08:45:03.652 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 17); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/78/ab0335f027acd1ec76521f5c9982ab]
Jun-25 08:45:03.673 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:45:03.674 [Task submitter] INFO  nextflow.Session - [6c/17e539] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 2)
Jun-25 08:45:13.853 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 16); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/d9/c6f95d676d95aea1604976d1d619a1]
Jun-25 08:45:13.943 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:45:13.943 [Task submitter] INFO  nextflow.Session - [57/6bcd76] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 20)
Jun-25 08:45:17.392 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 14); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/06/776613bfa69fb681a2610c6b843c68]
Jun-25 08:45:17.447 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:45:17.451 [Task submitter] INFO  nextflow.Session - [18/ae935c] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 19)
Jun-25 08:45:21.316 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 13); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/e5/f2538646f9064deb1a68273514a5e2]
Jun-25 08:45:21.425 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:45:21.425 [Task submitter] INFO  nextflow.Session - [d2/01a057] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 1)
Jun-25 08:46:02.648 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 9); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/17/081a9d828a72e288b84ceb1214d839]
Jun-25 08:46:18.921 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 12); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/a9/d21cbdefee37d1d8efd68d601b0525]
Jun-25 08:46:18.953 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:46:18.954 [Task submitter] INFO  nextflow.Session - [0c/b03f09] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)
Jun-25 08:46:22.985 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 37; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 11); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/a4/0b6a783cc9382b540a63e6c7cbd209]
Jun-25 08:46:25.951 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 10); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/25/45aaf1b2c6b7f973a6b808778df80f]
Jun-25 08:46:40.060 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 15); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/90/6758e120f8a9a1c744a5fbbb80bf32]
Jun-25 08:46:41.570 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 12 -- submitted tasks are shown below
~> TaskHandler[id: 30; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 7); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/69/dd68266b13ab089061b127db119243]
~> TaskHandler[id: 31; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 5); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/68/1856a35a9426f3babd76c50e401e7e]
~> TaskHandler[id: 29; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 8); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/15/e0ed1bd375b2d38f9130febff802cb]
~> TaskHandler[id: 36; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 3); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/83/3b2b8feb0f727355a7d6d360d71af4]
~> TaskHandler[id: 32; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 4); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/5a/bd2c4618c378b6add632eee0ac3a42]
~> TaskHandler[id: 41; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 22); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/f8/4d8ddb7bd8f262e05ac63d94498b7e]
~> TaskHandler[id: 42; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 6); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ea/6a9eb08839544b942e2051413edac1]
~> TaskHandler[id: 44; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 2); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/6c/17e539546864b21046e4b232fb2488]
~> TaskHandler[id: 43; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 20); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/57/6bcd76bc811dd6d19464e2f3b51479]
~> TaskHandler[id: 45; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 19); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/18/ae935c1e4f2186619fda54ebfbfbb0]
.. remaining tasks omitted.
Jun-25 08:46:49.304 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 8); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/15/e0ed1bd375b2d38f9130febff802cb]
Jun-25 08:46:51.591 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 7); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/69/dd68266b13ab089061b127db119243]
Jun-25 08:47:24.062 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 5); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/68/1856a35a9426f3babd76c50e401e7e]
Jun-25 08:47:43.109 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 3); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/83/3b2b8feb0f727355a7d6d360d71af4]
Jun-25 08:48:17.371 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 22); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/f8/4d8ddb7bd8f262e05ac63d94498b7e]
Jun-25 08:49:06.691 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 4); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/5a/bd2c4618c378b6add632eee0ac3a42]
Jun-25 08:49:56.901 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 43; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 20); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/57/6bcd76bc811dd6d19464e2f3b51479]
Jun-25 08:50:06.869 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 45; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 19); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/18/ae935c1e4f2186619fda54ebfbfbb0]
Jun-25 08:51:41.587 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 4 -- submitted tasks are shown below
~> TaskHandler[id: 42; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 6); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ea/6a9eb08839544b942e2051413edac1]
~> TaskHandler[id: 44; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 2); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/6c/17e539546864b21046e4b232fb2488]
~> TaskHandler[id: 46; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 1); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/d2/01a05786f6ed6ab26367b2ba41c65f]
~> TaskHandler[id: 47; name: PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1); status: RUNNING; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/0c/b03f09bb5e3364ac878c79e5254c4b]
Jun-25 08:52:02.926 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 42; name: PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (AFcohortHG19 chromosome 6); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/ea/6a9eb08839544b942e2051413edac1]
Jun-25 08:52:40.683 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 47; name: PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1); status: COMPLETED; exit: 0; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/0c/b03f09bb5e3364ac878c79e5254c4b]
Jun-25 08:52:40.812 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:52:40.812 [Task submitter] INFO  nextflow.Session - [aa/f18a47] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 8)
Jun-25 08:52:40.849 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:52:40.849 [Task submitter] INFO  nextflow.Session - [72/612d5e] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 9)
Jun-25 08:52:40.868 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:52:40.868 [Task submitter] INFO  nextflow.Session - [84/a3bd1f] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 5)
Jun-25 08:52:40.884 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:52:40.884 [Task submitter] INFO  nextflow.Session - [a2/aed86c] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 3)
Jun-25 08:52:40.905 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:52:40.905 [Task submitter] INFO  nextflow.Session - [f4/b5cfff] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 7)
Jun-25 08:52:40.930 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:52:40.931 [Task submitter] INFO  nextflow.Session - [a5/4f69f3] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)
Jun-25 08:52:40.962 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:52:40.962 [Task submitter] INFO  nextflow.Session - [9e/4ace7e] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 11)
Jun-25 08:52:40.964 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 15 -- tasks to be submitted are shown below
~> TaskHandler[id: 63; name: PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 21); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/88/53f0051c30303eed897478baf1743a]
~> TaskHandler[id: 51; name: PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 10); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/99/21be857ed251430d1f14060dc6b6a3]
~> TaskHandler[id: 57; name: PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 12); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/8c/470f006f43f17ed6bfd199bba71279]
~> TaskHandler[id: 58; name: PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 13); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/12/9255762bc1b9629b2807027a5aaf98]
~> TaskHandler[id: 62; name: PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 17); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/6f/cf204e555ca5c4562388a817776a09]
~> TaskHandler[id: 61; name: PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 18); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/a8/bf3f8b8f78454057890c6df5fe06d1]
~> TaskHandler[id: 49; name: PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 14); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/7c/4a0923c9d8d4c1ebe25be234370471]
~> TaskHandler[id: 55; name: PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 4); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/3f/6a868abf5c613179a49f0062be0706]
~> TaskHandler[id: 48; name: PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 15); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/c0/9435953905bc665ecd45eb96a96dd2]
~> TaskHandler[id: 68; name: PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 19); status: NEW; exit: -; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/b7/f28086aad4a168e24ca4087b9ef103]
.. remaining tasks omitted.
Jun-25 08:52:57.375 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 50; name: PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16); status: COMPLETED; exit: 1; error: -; workDir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/a5/4f69f378e510ce2001d4bd1262724d]
Jun-25 08:52:57.381 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16); work-dir=/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/a5/4f69f378e510ce2001d4bd1262724d
  error [nextflow.exception.ProcessFailedException]: Process `PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)` terminated with an error exit status (1)
Jun-25 08:52:57.391 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-25 08:52:57.391 [Task submitter] INFO  nextflow.Session - [88/53f005] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 21)
Jun-25 08:52:57.462 [TaskFinalizer-6] ERROR nextflow.processor.TaskProcessor - Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)'

Caused by:
  Process `PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (AFcohortHG19 chromosome 16)` terminated with an error exit status (1)

Command executed:

  export POLARS_MAX_THREADS=2

  pgscatalog-match                  --dataset AFcohortHG19         --scorefile scorefiles.txt.gz         --target GRCh37_AFcohortHG19_16.pvar.zst         --only_match         --chrom 16                           --outdir $PWD         -v

  cat <<-END_VERSIONS > versions.yml
  MATCH_VARIANTS:
      pgscatalog.match: $(echo $(python -c 'import pgscatalog.match; print(pgscatalog.match.__version__)'))
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  pgscatalog.match.cli.match_cli: 2024-06-25 08:52:43 WARNING  No output format specified, writing to combined scoring file
  pgscatalog.match.cli.match_cli: 2024-06-25 08:52:43 DEBUG    Verbose logging enabled
  pgscatalog.match.cli.match_cli: 2024-06-25 08:52:43 INFO     --cleanup set (default), temporary files will be deleted
  pgscatalog.match.lib.scoringfileframe: 2024-06-25 08:52:43 DEBUG    Converting ScoringFileFrame(NormalisedScoringFile('scorefiles.txt.gz')) to feather format
  pgscatalog.match.lib.scoringfileframe: 2024-06-25 08:52:54 DEBUG    ScoringFileFrame(NormalisedScoringFile('scorefiles.txt.gz')) feather conversion complete
  pgscatalog.match.lib._match.preprocess: 2024-06-25 08:52:55 DEBUG    Complementing column effect_allele
  pgscatalog.match.lib._match.preprocess: 2024-06-25 08:52:55 DEBUG    Complementing column other_allele
  pgscatalog.match.lib.scoringfileframe: 2024-06-25 08:52:55 DEBUG    Filtering scoring file to chromosome 16
  pgscatalog.match.lib.variantframe: 2024-06-25 08:52:55 DEBUG    Converting VariantFrame(path='GRCh37_AFcohortHG19_16.pvar.zst', dataset='AFcohortHG19', chrom='16', cleanup=True, tmpdir=PosixPath('tmp')) to feather format
  Traceback (most recent call last):
    File "/app/pgscatalog.utils/.venv/bin/pgscatalog-match", line 8, in <module>
      sys.exit(run_match())
               ^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/cli/match_cli.py", line 87, in run_match
      ipc_path = get_match_candidates(
                 ^^^^^^^^^^^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/cli/match_cli.py", line 124, in get_match_candidates
      with variants as target_df:
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/lib/variantframe.py", line 54, in __enter__
      self.arrowpaths = loose(self.variants, tmpdir=self._tmpdir)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/functools.py", line 909, in wrapper
      return dispatch(args[0].__class__)(*args, **kw)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/lib/_arrow.py", line 94, in _
      return batch_read(reader, tmpdir=tmpdir, cols_keep=cols_keep)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/lib/_arrow.py", line 102, in batch_read
      batches = reader.next_batches(batch_size)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/polars/io/csv/batched_reader.py", line 134, in next_batches
      batches = self._reader.next_batches(n)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  polars.exceptions.ComputeError: found more fields than defined in 'Schema'

  Consider setting 'truncate_ragged_lines=True'.
  Exception ignored in atexit callback: <function _exit at 0x2aaaab5580e0>
  Traceback (most recent call last):
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/cli/match_cli.py", line 31, in _exit
      shutil.rmtree(Config.MATCHTMP)
    File "/usr/local/lib/python3.11/shutil.py", line 763, in rmtree
      onerror(os.rmdir, path, sys.exc_info())
    File "/usr/local/lib/python3.11/shutil.py", line 761, in rmtree
      os.rmdir(path, dir_fd=dir_fd)
  OSError: [Errno 39] Directory not empty: 'matchtmp'

Work dir:
  /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/a5/4f69f378e510ce2001d4bd1262724d

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Jun-25 08:52:57.475 [TaskFinalizer-6] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Jun-25 08:52:57.510 [main] DEBUG nextflow.Session - Session await > all processes finished
Jun-25 08:52:57.551 [Actor Thread 8] ERROR nextflow.Nextflow - ERROR: Projection subworkflow failed
Jun-25 08:52:57.560 [Actor Thread 30] ERROR nextflow.Nextflow - ERROR: Matching subworkflow failed
Jun-25 08:52:57.565 [Actor Thread 21] ERROR nextflow.Nextflow - ERROR: No scores calculated!
Jun-25 08:52:57.569 [Actor Thread 17] ERROR nextflow.Nextflow - ERROR: No results report written!
$ cat work/a5/4f69f378e510ce2001d4bd1262724d/.command.sh
#!/bin/bash -euo pipefail
export POLARS_MAX_THREADS=2

pgscatalog-match                  --dataset AFcohortHG19         --scorefile scorefiles.txt.gz         --target GRCh37_AFcohortHG19_16.pvar.zst         --only_match         --chrom 16                           --outdir $PWD         -v

cat <<-END_VERSIONS > versions.yml
MATCH_VARIANTS:
    pgscatalog.match: $(echo $(python -c 'import pgscatalog.match; print(pgscatalog.match.__version__)'))
END_VERSIONS
Carldeboer commented 5 days ago

Doesn't seem to be the chr22/22 thing - just tested it with chr and it also died, seemingly at the same spot.

nebfield commented 5 days ago

By default plink will strip out chr prefixes during recoding and relabelling, and the target genomes will be made compatible with the reference panel automatically.

Thanks for the logs. The most interesting exception is here:

    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/lib/_arrow.py", line 94, in _
      return batch_read(reader, tmpdir=tmpdir, cols_keep=cols_keep)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/lib/_arrow.py", line 102, in batch_read
      batches = reader.next_batches(batch_size)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/polars/io/csv/batched_reader.py", line 134, in next_batches
      batches = self._reader.next_batches(n)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  polars.exceptions.ComputeError: found more fields than defined in 'Schema'

It seems like the pvar files has some unexpected columns, probably left over from the VCF recoding.

What are the column names in some of your pvar files?

Truongphikt commented 20 hours ago

By default plink will strip out chr prefixes during recoding and relabelling, and the target genomes will be made compatible with the reference panel automatically.

Thanks for the logs. The most interesting exception is here:

    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/lib/_arrow.py", line 94, in _
      return batch_read(reader, tmpdir=tmpdir, cols_keep=cols_keep)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/lib/_arrow.py", line 102, in batch_read
      batches = reader.next_batches(batch_size)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/polars/io/csv/batched_reader.py", line 134, in next_batches
      batches = self._reader.next_batches(n)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  polars.exceptions.ComputeError: found more fields than defined in 'Schema'

It seems like the pvar files has some unexpected columns, probably left over from the VCF recoding.

What are the column names in some of your pvar files?

I have the same problem when running with VCF files. My sample sheet:

sampleset,path_prefix,chrom,format
testdata,/home/test_data/glimpse2_merged/1_merged_glimpse,1,vcf
testdata,/home/test_data/glimpse2_merged/2_merged_glimpse,2,vcf
testdata,/home/test_data/glimpse2_merged/3_merged_glimpse,3,vcf
...

The path of the vcf files is /home/test_data/glimpse2_merged/1_merged_glimpse.vcf.gz. This is the first 50 lines of one vcf file: head_vcf.txt

I ran the pipeline and failed: screen.log After that, I get in the workDir of an arbitrary error process to debugging: command.run.log

Could you tell me what thing I did wrong? Possible causes and how to fix this issue? Thank you.