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"2 missing chromosomes detected! Maximum is 1. Check your samplesheet." when using a combined samplesheet #323

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Carldeboer opened this issue Jun 19, 2024 · 3 comments · Fixed by #322
Closed

"2 missing chromosomes detected! Maximum is 1. Check your samplesheet." when using a combined samplesheet #323

Carldeboer opened this issue Jun 19, 2024 · 3 comments · Fixed by #322
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@nebfield
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bug Something isn't working

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@Carldeboer
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Description of the bug

When running pgsc_calc on a samplesheet with multiple sampleset, I get the error: 2 missing chromosomes detected! Maximum is 1. Check your samplesheet.. Splitting the file into two, each with only one sampleset works fine.

Command used and terminal output

$ nextflow run pgscatalog/pgsc_calc -profile apptainer --input AF_cohort_samplesheet.hg38.CD.txt  --target_build GRCh38 --pgs_id PGS000016,PGS002814 --outdir AF_cohort_AF_PGSs_hg38
... works fine
$ nextflow run pgscatalog/pgsc_calc -profile apptainer --input AF_cohort_samplesheet.hg38.cohort.txt  --target_build GRCh38 --pgs_id PGS000016,PGS002814 --outdir AF_cohort_AF_PGSs_hg38
... works fine
$ nextflow run pgscatalog/pgsc_calc -profile apptainer --input AF_cohort_samplesheet.hg38.txt  --target_build GRCh38 --pgs_id PGS000016,PGS002814 --outdir AF_cohort_AF_PGSs_hg38

 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NOTE: Your local project version looks outdated - a different revision is available in the remote repository [ca334fa575]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` [chaotic_swartz] 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           : chaotic_swartz
  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/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc
  userName          : cdeboer
  profile           : apptainer
  configFiles       :

Input/output options
  input             : AF_cohort_samplesheet.hg38.txt
  pgs_id            : PGS000016,PGS002814
  outdir            : AF_cohort_AF_PGSs_hg38

Reference options
  ref_samplesheet   : /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
  ld_grch37         : /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
  ld_grch38         : /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
  ancestry_checksums: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/assets/ancestry/checksums.txt

Compatibility options
  target_build      : GRCh38

!! 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

[-        ] 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:MATCH:MATCH_VARIANTS               -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE                -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE           -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE        -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT                -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS               -
2 missing chromosomes detected! Maximum is 1. Check your samplesheet.
ERROR ~ ERROR: No results report written!

 -- 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

$ cat AF_cohort_samplesheet.hg38.txt
sampleset,path_prefix,chrom,format
AFcohortHG38,hg38_vcfs/1.hg38,1,vcf
AFcohortHG38,hg38_vcfs/2.hg38,2,vcf
AFcohortHG38,hg38_vcfs/3.hg38,3,vcf
AFcohortHG38,hg38_vcfs/4.hg38,4,vcf
AFcohortHG38,hg38_vcfs/5.hg38,5,vcf
AFcohortHG38,hg38_vcfs/6.hg38,6,vcf
AFcohortHG38,hg38_vcfs/7.hg38,7,vcf
AFcohortHG38,hg38_vcfs/8.hg38,8,vcf
AFcohortHG38,hg38_vcfs/9.hg38,9,vcf
AFcohortHG38,hg38_vcfs/10.hg38,10,vcf
AFcohortHG38,hg38_vcfs/11.hg38,11,vcf
AFcohortHG38,hg38_vcfs/12.hg38,12,vcf
AFcohortHG38,hg38_vcfs/13.hg38,13,vcf
AFcohortHG38,hg38_vcfs/14.hg38,14,vcf
AFcohortHG38,hg38_vcfs/15.hg38,15,vcf
AFcohortHG38,hg38_vcfs/16.hg38,16,vcf
AFcohortHG38,hg38_vcfs/17.hg38,17,vcf
AFcohortHG38,hg38_vcfs/18.hg38,18,vcf
AFcohortHG38,hg38_vcfs/19.hg38,19,vcf
AFcohortHG38,hg38_vcfs/20.hg38,20,vcf
AFcohortHG38,hg38_vcfs/21.hg38,21,vcf
AFcohortHG38,hg38_vcfs/22.hg38,22,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr1.hg38,1,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr2.hg38,2,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr3.hg38,3,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr4.hg38,4,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr5.hg38,5,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr6.hg38,6,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr7.hg38,7,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr8.hg38,8,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr9.hg38,9,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr10.hg38,10,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr11.hg38,11,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr12.hg38,12,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr13.hg38,13,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr14.hg38,14,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr15.hg38,15,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr16.hg38,16,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr17.hg38,17,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr18.hg38,18,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr19.hg38,19,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr20.hg38,20,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr21.hg38,21,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr22.hg38,22,vcf
$ cat AF_cohort_samplesheet.hg38.CD.txt
sampleset,path_prefix,chrom,format
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr1.hg38,1,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr2.hg38,2,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr3.hg38,3,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr4.hg38,4,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr5.hg38,5,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr6.hg38,6,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr7.hg38,7,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr8.hg38,8,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr9.hg38,9,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr10.hg38,10,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr11.hg38,11,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr12.hg38,12,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr13.hg38,13,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr14.hg38,14,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr15.hg38,15,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr16.hg38,16,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr17.hg38,17,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr18.hg38,18,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr19.hg38,19,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr20.hg38,20,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr21.hg38,21,vcf
CDHG38,../Genotypes/20221206_liftover_VCFs/CD.chr22.hg38,22,vcf
$ cat AF_cohort_samplesheet.hg38.cohort.txt
sampleset,path_prefix,chrom,format
AFcohortHG38,hg38_vcfs/1.hg38,1,vcf
AFcohortHG38,hg38_vcfs/2.hg38,2,vcf
AFcohortHG38,hg38_vcfs/3.hg38,3,vcf
AFcohortHG38,hg38_vcfs/4.hg38,4,vcf
AFcohortHG38,hg38_vcfs/5.hg38,5,vcf
AFcohortHG38,hg38_vcfs/6.hg38,6,vcf
AFcohortHG38,hg38_vcfs/7.hg38,7,vcf
AFcohortHG38,hg38_vcfs/8.hg38,8,vcf
AFcohortHG38,hg38_vcfs/9.hg38,9,vcf
AFcohortHG38,hg38_vcfs/10.hg38,10,vcf
AFcohortHG38,hg38_vcfs/11.hg38,11,vcf
AFcohortHG38,hg38_vcfs/12.hg38,12,vcf
AFcohortHG38,hg38_vcfs/13.hg38,13,vcf
AFcohortHG38,hg38_vcfs/14.hg38,14,vcf
AFcohortHG38,hg38_vcfs/15.hg38,15,vcf
AFcohortHG38,hg38_vcfs/16.hg38,16,vcf
AFcohortHG38,hg38_vcfs/17.hg38,17,vcf
AFcohortHG38,hg38_vcfs/18.hg38,18,vcf
AFcohortHG38,hg38_vcfs/19.hg38,19,vcf
AFcohortHG38,hg38_vcfs/20.hg38,20,vcf
AFcohortHG38,hg38_vcfs/21.hg38,21,vcf
AFcohortHG38,hg38_vcfs/22.hg38,22,vcf

Relevant files

$ cat .nextflow.log
Jun-19 12:55:39.037 [main] DEBUG nextflow.cli.Launcher - $> nextflow run pgscatalog/pgsc_calc -profile apptainer --input AF_cohort_samplesheet.hg38.CD.txt --target_build GRCh38 --pgs_id PGS000016,PGS002814 --outdir AF_cohort_AF_PGSs_hg38
Jun-19 12:55:39.255 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.2
Jun-19 12:55:39.286 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/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 12:55:39.313 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-19 12:55:39.315 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-19 12:55:39.320 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Jun-19 12:55:39.342 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jun-19 12:55:39.364 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/scm
Jun-19 12:55:40.680 [main] DEBUG nextflow.scm.AssetManager - Git config: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/.git/config; branch: main; remote: origin; url: https://github.com/PGScatalog/pgsc_calc.git
Jun-19 12:55:40.722 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jun-19 12:55:40.741 [main] DEBUG nextflow.scm.AssetManager - Git config: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/.git/config; branch: main; remote: origin; url: https://github.com/PGScatalog/pgsc_calc.git
Jun-19 12:55:41.814 [main] INFO nextflow.scm.AssetManager - NOTE: Your local project version looks outdated - a different revision is available in the remote repository [ca334fa]
Jun-19 12:55:41.828 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/nextflow.config
Jun-19 12:55:41.831 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/nextflow.config
Jun-19 12:55:41.840 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/secrets/store.json
Jun-19 12:55:41.843 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@c412556] - activable => nextflow.secret.LocalSecretsProvider@c412556
Jun-19 12:55:41.856 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: apptainer
Jun-19 12:55:42.744 [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 12:55:42.796 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jun-19 12:55:42.798 [main] DEBUG nextflow.cli.CmdRun - Launching https://github.com/pgscatalog/pgsc_calc [ridiculous_mendel] DSL2 - revision: 45326ac [main]
Jun-19 12:55:42.800 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-19 12:55:42.800 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jun-19 12:55:42.905 [main] DEBUG nextflow.Session - Session UUID: b0e06bb6-062a-46ab-b10f-9acfd5f9153a
Jun-19 12:55:42.906 [main] DEBUG nextflow.Session - Run name: ridiculous_mendel
Jun-19 12:55:42.906 [main] DEBUG nextflow.Session - Executor pool size: 16
Jun-19 12:55:42.921 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jun-19 12:55:42.929 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-19 12:55:42.963 [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: 166211@login02 [206.12.119.244]
CPUs: 16 - Mem: 187.5 GB (1.7 GB) - Swap: 0 (0)
Jun-19 12:55:43.005 [main] DEBUG nextflow.Session - Work-dir: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work [nfs]
Jun-19 12:55:43.006 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/bin
Jun-19 12:55:43.025 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-19 12:55:43.041 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-19 12:55:43.158 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-19 12:55:43.177 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 17; maxThreads: 1000
Jun-19 12:55:43.326 [main] DEBUG nextflow.Session - Session start
Jun-19 12:55:43.329 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/AF_cohort_AF_PGSs_hg38/pipeline_info/execution_trace_2024-06-19_12-55-42.txt
Jun-19 12:55:43.343 [main] DEBUG nextflow.Session - Using default localLib path: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/lib
Jun-19 12:55:43.349 [main] DEBUG nextflow.Session - Adding to the classpath library: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/lib
Jun-19 12:55:44.065 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-19 12:55:44.904 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: latest
Jun-19 12:55:45.055 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-validation@1.1.3' resolved
Jun-19 12:55:45.056 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-validation@1.1.3'
Jun-19 12:55:45.078 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-validation@1.1.3
Jun-19 12:55:45.080 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation
Jun-19 12:55:45.170 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter monochromeLogs -- Initialise it to a default value eg. params.monochromeLogs = some_value
Jun-19 12:55:45.177 [main] INFO nextflow.Nextflow -

pgscatalog/pgsc_calc v2.0.0-alpha.6-g45326ac

Core Nextflow options
revision : main
runName : ridiculous_mendel
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/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc
userName : cdeboer
profile : apptainer
configFiles :

Input/output options
input : AF_cohort_samplesheet.hg38.CD.txt
pgs_id : PGS000016,PGS002814
outdir : AF_cohort_AF_PGSs_hg38

Reference options
ref_samplesheet : /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
ld_grch37 : /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
ld_grch38 : /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
ancestry_checksums: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/assets/ancestry/checksums.txt

Compatibility options
target_build : GRCh38

!! Only displaying parameters that differ from the pipeline defaults !!

If you use pgscatalog/pgsc_calc for your analysis please cite:

Jun-19 12:55:51.023 [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 12:55:51.026 [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 12:55:51.053 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 12:55:51.054 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 12:55:51.064 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jun-19 12:55:51.073 [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 12:55:51.077 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jun-19 12:55:51.434 [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 12:55:51.435 [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 12:55:51.436 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:COMBINE_SCOREFILES matches process PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES
Jun-19 12:55:51.439 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 12:55:51.439 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 12:55:51.515 [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 12:55:51.515 [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 12:55:51.517 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:PLINK2_RELABELBIM matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM
Jun-19 12:55:51.525 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 12:55:51.525 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 12:55:51.553 [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 12:55:51.554 [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 12:55:51.555 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:PLINK2_RELABELPVAR matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR
Jun-19 12:55:51.558 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 12:55:51.558 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 12:55:51.581 [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 12:55:51.582 [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 12:55:51.583 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:PLINK2_VCF matches process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF
Jun-19 12:55:51.587 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 12:55:51.587 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 12:55:51.662 [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 12:55:51.663 [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 12:55:51.664 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:MATCH_VARIANTS|MATCH_COMBINE matches process PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-19 12:55:51.668 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 12:55:51.668 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 12:55:51.719 [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 12:55:51.720 [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 12:55:51.721 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:MATCH_VARIANTS|MATCH_COMBINE matches process PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-19 12:55:51.723 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 12:55:51.723 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 12:55:51.787 [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 12:55:51.787 [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 12:55:51.787 [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 12:55:51.788 [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 12:55:51.789 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:PLINK2_SCORE matches process PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-19 12:55:51.792 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 12:55:51.792 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 12:55:51.823 [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 12:55:51.825 [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 12:55:51.827 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 12:55:51.827 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 12:55:51.874 [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 12:55:51.874 [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 12:55:51.875 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:PGSCATALOG_GET|SCORE_REPORT matches process PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-19 12:55:51.877 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 12:55:51.877 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 12:55:51.920 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:pyyaml matches labels pyyaml for process with name PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS
Jun-19 12:55:51.921 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:DUMPSOFTWAREVERSIONS matches process PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS
Jun-19 12:55:51.923 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-19 12:55:51.923 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-19 12:55:51.928 [main] DEBUG nextflow.Session - Config process names validation disabled as requested
Jun-19 12:55:51.931 [main] DEBUG nextflow.Session - Igniting dataflow network (32)
Jun-19 12:55:51.932 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES
Jun-19 12:55:51.944 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES
Jun-19 12:55:51.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM
Jun-19 12:55:51.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR
Jun-19 12:55:51.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF
Jun-19 12:55:51.953 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS
Jun-19 12:55:51.955 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE
Jun-19 12:55:51.957 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE
Jun-19 12:55:51.957 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE
Jun-19 12:55:51.959 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT
Jun-19 12:55:51.959 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS
Jun-19 12:55:51.964 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_ac673998bae353b8: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/intersect_variants.nf
Script_4b4c11c4fe56d274: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/match_variants.nf
Script_427b79f8ec452926: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/extract_database.nf
Script_6ee8db14b0ece2bc: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/main.nf
Script_a9598b3d758285aa: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/score_aggregate.nf
Script_b4ded561a904b4b9: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/pgsc_calc.nf
Script_951dc19390c5c741: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/combine_scorefiles.nf
Script_1317eccf6cefc502: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/ancestry_project.nf
Script_12c9a6a07f86b4fa: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../modules/local/download_scorefiles.nf
Script_c7b87f734d3160d0: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/fraposa_project.nf
Script_67ef02006e15f7bf: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/bootstrap/make_database.nf
Script_e72266e4c23a6709: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/bootstrap_ancestry.nf
Script_85d9c5de3f9419f5: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_score.nf
Script_0590bc8b268609ac: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/relabel_ids.nf
Script_dd9e9d3067ae34d9: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_vcf.nf
Script_7877cbba589aaba3: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_relabelbim.nf
Script_ddfebfdd3f2163fa: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/intersect_thinned.nf
Script_fd7831fa32f2ed40: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/ancestry/relabel_afreq.nf
Script_1325f56916418255: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/plink2_relabelpvar.nf
Script_0fa47898366f4cc3: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/make_compatible.nf
Script_e8e89f1db16463e9: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/input_check.nf
Script_dac204016b7d984d: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/match_combine.nf
Script_71125e7d812b2828: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/apply_score.nf
Script_8463068cf880c25a: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/ancestry/ancestry_analysis.nf
Script_7471b788f1a2a9d3: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/filter_variants.nf
Script_58fbd5e82e3df7c9: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/report.nf
Script_a1be163d058c7f54: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../modules/local/dumpsoftwareversions.nf
Script_5556e4a34f537c27: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/match.nf
Script_b5a82ee5e9eb54e0: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/plink2_makebed.nf
Script_dfec6a09ab0763d3: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/score_report.nf
Script_7237b9b1d4f9edb3: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/bootstrap/setup_resource.nf
Script_00d09c28a4e6e597: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/../../modules/local/ancestry/relabel_scorefiles.nf
Script_75119a130470a3ec: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/plink2_orient.nf
Script_1c509e4a65296f87: /arc/project/st-cdeboer-1/cdeboer/AFib/Genotypes/MY-PIPELINES20240614/assets/pgscatalog/pgsc_calc/./workflows/../subworkflows/local/ancestry/../../../modules/local/ancestry/oadp/fraposa_pca.nf
Jun-19 12:55:51.965 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jun-19 12:55:51.965 [main] DEBUG nextflow.Session - Session await
Jun-19 12:55:52.098 [Actor Thread 26] 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 12:55:52.118 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (2) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_2.pgen (pattern: GRCh38_CDHG38_2.pgen)
Jun-19 12:55:52.118 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (1) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_1.pgen (pattern: GRCh38_CDHG38_1.pgen)
Jun-19 12:55:52.118 [Actor Thread 5] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (3) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_3.pgen (pattern: GRCh38_CDHG38_3.pgen)
Jun-19 12:55:52.118 [Actor Thread 17] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (15) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_15.pgen (pattern: GRCh38_CDHG38_15.pgen)
Jun-19 12:55:52.118 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (10) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_10.pgen (pattern: GRCh38_CDHG38_10.pgen)
Jun-19 12:55:52.118 [Actor Thread 10] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (4) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_4.pgen (pattern: GRCh38_CDHG38_4.pgen)
Jun-19 12:55:52.119 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (7) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_7.pgen (pattern: GRCh38_CDHG38_7.pgen)
Jun-19 12:55:52.119 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (6) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_6.pgen (pattern: GRCh38_CDHG38_6.pgen)
Jun-19 12:55:52.120 [Actor Thread 19] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (14) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_14.pgen (pattern: GRCh38_CDHG38_14.pgen)
Jun-19 12:55:52.120 [Actor Thread 9] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (5) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_5.pgen (pattern: GRCh38_CDHG38_5.pgen)
Jun-19 12:55:52.120 [Actor Thread 4] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (9) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_9.pgen (pattern: GRCh38_CDHG38_9.pgen)
Jun-19 12:55:52.120 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (13) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_13.pgen (pattern: GRCh38_CDHG38_13.pgen)
Jun-19 12:55:52.121 [Actor Thread 3] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (11) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_11.pgen (pattern: GRCh38_CDHG38_11.pgen)
Jun-19 12:55:52.121 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (12) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_12.pgen (pattern: GRCh38_CDHG38_12.pgen)
Jun-19 12:55:52.121 [Actor Thread 21] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (16) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_16.pgen (pattern: GRCh38_CDHG38_16.pgen)
Jun-19 12:55:52.123 [Actor Thread 13] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (8) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_8.pgen (pattern: GRCh38_CDHG38_8.pgen)
Jun-19 12:55:52.140 [Actor Thread 23] 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-19 12:55:52.258 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (17) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_17.pgen (pattern: GRCh38_CDHG38_17.pgen)
Jun-19 12:55:52.265 [Actor Thread 17] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (18) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_18.pgen (pattern: GRCh38_CDHG38_18.pgen)
Jun-19 12:55:52.278 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (20) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_20.pgen (pattern: GRCh38_CDHG38_20.pgen)
Jun-19 12:55:52.282 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (22) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_22.pgen (pattern: GRCh38_CDHG38_22.pgen)
Jun-19 12:55:52.283 [Actor Thread 21] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (19) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_19.pgen (pattern: GRCh38_CDHG38_19.pgen)
Jun-19 12:55:52.293 [Actor Thread 13] DEBUG nextflow.processor.TaskProcessor - Process PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (21) is unable to find [UnixPath]: /arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/genomes/recoded/GRCh38_CDHG38_21.pgen (pattern: GRCh38_CDHG38_21.pgen)
Jun-19 12:55:52.340 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-19 12:55:52.343 [Task submitter] INFO nextflow.Session - [26/e40776] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (CDHG38 chromosome 12)
Jun-19 12:55:52.369 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-19 12:55:52.369 [Task submitter] INFO nextflow.Session - [bf/eecfb3] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (CDHG38 chromosome 15)
Jun-19 12:55:52.404 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-19 12:55:52.405 [Task submitter] INFO nextflow.Session - [02/9f2fcb] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (CDHG38 chromosome 16)
Jun-19 12:55:52.448 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-19 12:55:52.449 [Task submitter] INFO nextflow.Session - [c9/0c9f10] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (CDHG38 chromosome 13)
Jun-19 12:55:52.512 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-19 12:55:52.513 [Task submitter] INFO nextflow.Session - [1d/42005a] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (CDHG38 chromosome 8)
Jun-19 12:55:52.579 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-19 12:55:52.579 [Task submitter] INFO nextflow.Session - [56/835967] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (CDHG38 chromosome 2)
Jun-19 12:55:52.648 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-19 12:55:52.649 [Task submitter] INFO nextflow.Session - [4b/0be9c9] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (CDHG38 chromosome 5)
Jun-19 12:55:52.689 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-19 12:55:52.689 [Task submitter] INFO nextflow.Session - [61/56d55a] Submitted process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (CDHG38 chromosome 3)
Jun-19 12:55:55.069 [SIGINT handler] DEBUG nextflow.Session - Session aborted -- Cause: SIGINT
Jun-19 12:55:55.086 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jun-19 12:55:55.112 [SIGINT handler] DEBUG nextflow.Session - The following nodes are still active:
[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: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: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:SCORE_REPORT
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (queue) OPEN ; channel: intersect_count
port 2: (value) bound ; 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 12:55:55.115 [main] DEBUG nextflow.Session - Session await > all processes finished
Jun-19 12:55:55.115 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jun-19 12:55:55.129 [Actor Thread 15] ERROR nextflow.Nextflow - ERROR: Matching subworkflow failed
Jun-19 12:55:55.132 [Actor Thread 21] ERROR nextflow.Nextflow - ERROR: No scores calculated!
Jun-19 12:55:55.134 [Actor Thread 13] ERROR nextflow.Nextflow - ERROR: No results report written!
Jun-19 12:55:55.143 [Actor Thread 12] 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
@Carldeboer Carldeboer added the bug Something isn't working label Jun 19, 2024
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smlmbrt commented Jun 19, 2024

This is expected, we removed the functionality to score two datasets at once in version 2 as it became challenging to cache the reference sample overlaps with multiple target samples. It's best that they each have their own work & cache for easier debugging. If you wish to score them together the datasets should be merged and subsetted to variants that are common between both.

@smlmbrt smlmbrt added the user-query User queries & requests label Jun 19, 2024
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smlmbrt commented Jun 19, 2024

@nebfield, we should make the error message clearer here.

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yes, a clear error message would be very helpful. Thanks!

@nebfield nebfield added enhancement New feature or request and removed bug Something isn't working user-query User queries & requests labels Jun 20, 2024
@nebfield nebfield linked a pull request Jun 20, 2024 that will close this issue
Fix samplesheet parsing error warnings #322
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@nebfield nebfield added bug Something isn't working and removed enhancement New feature or request labels Jun 20, 2024
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Fix samplesheet parsing error warnings PGScatalog/pgsc_calc
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@smlmbrt @Carldeboer @nebfield