Oct-11 09:39:12.750 [main] DEBUG nextflow.cli.Launcher - $> nextflow run pgscatalog/pgsc_calc -profile singularity --input ../config/hgdp_tgp_samplesheet.csv --pgs_id PGS002250 --target_build GRCh38 --min_overlap 0.01 Oct-11 09:39:12.820 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.3 Oct-11 09:39:12.840 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/abiddan1/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.4 Oct-11 09:39:12.850 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Oct-11 09:39:12.851 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Oct-11 09:39:12.855 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Oct-11 09:39:12.865 [main] INFO org.pf4j.AbstractPluginManager - No plugins Oct-11 09:39:12.881 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/abiddan1/.nextflow/scm Oct-11 09:39:13.802 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc/.git/config; branch: main; remote: origin; url: https://github.com/PGScatalog/pgsc_calc.git Oct-11 09:39:13.821 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Oct-11 09:39:13.829 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc/.git/config; branch: main; remote: origin; url: https://github.com/PGScatalog/pgsc_calc.git Oct-11 09:39:14.511 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc/nextflow.config Oct-11 09:39:14.512 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc/nextflow.config Oct-11 09:39:14.525 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity` Oct-11 09:39:14.876 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [test_json, gitpod, debug, shifter, test, mamba, charliecloud, conda, singularity, test_full, docker, podman] Oct-11 09:39:14.910 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion Oct-11 09:39:14.911 [main] INFO nextflow.cli.CmdRun - Launching `https://github.com/pgscatalog/pgsc_calc` [pedantic_kowalevski] DSL2 - revision: 863166865e [main] Oct-11 09:39:14.911 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Oct-11 09:39:14.911 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Oct-11 09:39:14.915 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/abiddan1/.nextflow/secrets/store.json Oct-11 09:39:14.918 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@20256a0b] - activable => nextflow.secret.LocalSecretsProvider@20256a0b Oct-11 09:39:14.982 [main] DEBUG nextflow.Session - Session UUID: 7b478047-1f5e-4c9e-a9ef-ba416b5e49db Oct-11 09:39:14.982 [main] DEBUG nextflow.Session - Run name: pedantic_kowalevski Oct-11 09:39:14.983 [main] DEBUG nextflow.Session - Executor pool size: 48 Oct-11 09:39:14.994 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=144; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Oct-11 09:39:15.018 [main] DEBUG nextflow.cli.CmdRun - Version: 23.04.3 build 5875 Created: 11-08-2023 18:37 UTC (14:37 EDT) System: Linux 4.18.0-372.9.1.el8.x86_64 Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 11.0.13+7-b1751.21 Encoding: UTF-8 (UTF-8) Process: 588464@devrmccoy1 [172.20.4.3] CPUs: 48 - Mem: 1.5 TB (1.4 TB) - Swap: 0 (0) Oct-11 09:39:15.036 [main] DEBUG nextflow.Session - Work-dir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work [gpfs] Oct-11 09:39:15.058 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Oct-11 09:39:15.069 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Oct-11 09:39:15.146 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Oct-11 09:39:15.157 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 49; maxThreads: 1000 Oct-11 09:39:15.291 [main] DEBUG nextflow.Session - Session start Oct-11 09:39:15.299 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/results/pipeline_info/execution_trace_2023-10-11_09-39-14.txt Oct-11 09:39:15.310 [main] DEBUG nextflow.Session - Using default localLib path: /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc/lib Oct-11 09:39:15.313 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc/lib Oct-11 09:39:15.314 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc/lib/nfcore_external_java_deps.jar Oct-11 09:39:16.029 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Oct-11 09:39:16.191 [main] WARN nextflow.Nextflow - Found unexpected parameters: * --ref_format_version: v0.1 * --ancestry_checksums: /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/checksums.txt Oct-11 09:39:16.192 [main] INFO nextflow.Nextflow - - Ignore this warning: params.schema_ignore_params = "ref_format_version,ancestry_checksums"  Oct-11 09:39:16.204 [main] INFO nextflow.Nextflow - ------------------------------------------------------  pgscatalog/pgsc_calc v2.0.0-alpha.2 ------------------------------------------------------ Core Nextflow options revision : main runName : pedantic_kowalevski containerEngine : singularity launchDir : /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline workDir : /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work projectDir : /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc userName : abiddan1 profile : singularity configFiles : /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc/nextflow.config Input/output options input : ../config/hgdp_tgp_samplesheet.csv pgs_id : PGS002250 genotypes_cache : null Reference options run_ancestry : null ref_samplesheet : /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv ld_grch37 : /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt ld_grch38 : /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt Compatibility options target_build : GRCh38 Matching options min_overlap : 0.01 Max job request options max_cpus : 2 max_memory : 16.GB Other parameters ancestry_checksums: /home/abiddan1/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/checksums.txt !! 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 ------------------------------------------------------ Oct-11 09:39:20.242 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES Oct-11 09:39:20.243 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES Oct-11 09:39:20.249 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-11 09:39:20.249 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-11 09:39:20.255 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Oct-11 09:39:20.260 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=48; memory=1.5 TB; capacity=48; pollInterval=100ms; dumpInterval=5m Oct-11 09:39:20.370 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,pgscatalog_utils` for process with name PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON Oct-11 09:39:20.371 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_low,pgscatalog_utils` for process with name PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON Oct-11 09:39:20.372 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-11 09:39:20.372 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-11 09:39:20.409 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:COMBINE_SCOREFILES Oct-11 09:39:20.409 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:COMBINE_SCOREFILES Oct-11 09:39:20.409 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COMBINE_SCOREFILES` matches process PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:COMBINE_SCOREFILES Oct-11 09:39:20.410 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-11 09:39:20.410 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-11 09:39:20.458 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM Oct-11 09:39:20.459 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM Oct-11 09:39:20.459 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_RELABELBIM` matches process PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM Oct-11 09:39:20.460 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-11 09:39:20.460 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-11 09:39:20.473 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR Oct-11 09:39:20.474 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_low,plink2` for process with name PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR Oct-11 09:39:20.474 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_RELABELPVAR` matches process PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR Oct-11 09:39:20.475 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-11 09:39:20.475 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-11 09:39:20.491 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,plink2` for process with name PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF Oct-11 09:39:20.491 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_medium,plink2` for process with name PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF Oct-11 09:39:20.492 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_VCF` matches process PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF Oct-11 09:39:20.493 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-11 09:39:20.493 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-11 09:39:20.544 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS Oct-11 09:39:20.544 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,pgscatalog_utils` for process with name PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS Oct-11 09:39:20.544 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MATCH_VARIANTS|MATCH_COMBINE` matches process PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS Oct-11 09:39:20.545 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-11 09:39:20.545 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-11 09:39:20.565 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,error_retry,pgscatalog_utils` for process with name PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE Oct-11 09:39:20.566 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches labels `process_medium,error_retry,pgscatalog_utils` for process with name PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE Oct-11 09:39:20.566 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_medium,error_retry,pgscatalog_utils` for process with name PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE Oct-11 09:39:20.566 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MATCH_VARIANTS|MATCH_COMBINE` matches process PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE Oct-11 09:39:20.567 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-11 09:39:20.567 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-11 09:39:20.586 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE Oct-11 09:39:20.586 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE Oct-11 09:39:20.586 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE Oct-11 09:39:20.586 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:plink2` matches labels `process_low,process_long,error_retry,plink2` for process with name PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE Oct-11 09:39:20.587 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLINK2_SCORE` matches process PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE Oct-11 09:39:20.587 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-11 09:39:20.587 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-11 09:39:20.595 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,pgscatalog_utils` for process with name PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:SCORE_AGGREGATE Oct-11 09:39:20.596 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pgscatalog_utils` matches labels `process_high_memory,pgscatalog_utils` for process with name PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:SCORE_AGGREGATE Oct-11 09:39:20.596 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-11 09:39:20.597 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-11 09:39:20.613 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high_memory,report` for process with name PGSCATALOG_PGSCALC:PGSCALC:REPORT:SCORE_REPORT Oct-11 09:39:20.613 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:report` matches labels `process_high_memory,report` for process with name PGSCATALOG_PGSCALC:PGSCALC:REPORT:SCORE_REPORT Oct-11 09:39:20.613 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PGSCATALOG_GET|SCORE_REPORT` matches process PGSCATALOG_PGSCALC:PGSCALC:REPORT:SCORE_REPORT Oct-11 09:39:20.614 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-11 09:39:20.614 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-11 09:39:20.632 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pyyaml` matches labels `pyyaml` for process with name PGSCATALOG_PGSCALC:PGSCALC:DUMPSOFTWAREVERSIONS Oct-11 09:39:20.633 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DUMPSOFTWAREVERSIONS` matches process PGSCATALOG_PGSCALC:PGSCALC:DUMPSOFTWAREVERSIONS Oct-11 09:39:20.633 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-11 09:39:20.634 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-11 09:39:20.636 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: PGSCATALOG_PGSCALC:PGSCALC:DUMPSOFTWAREVERSIONS, MATCH_COMBINE, INTERSECT_VARIANTS, PLINK2_RELABELPVAR, FRAPOSA_PCA, PLINK2_ORIENT, PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS, DUMPSOFTWAREVERSIONS, RELABEL_AFREQ_IDS, PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE, FILTER_VARIANTS, SAMPLESHEET_JSON, INTERSECT_THINNED, PGSCATALOG_PGSCALC:PGSCALC:REPORT:SCORE_REPORT, PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:COMBINE_SCOREFILES, COMBINE_SCOREFILES, SCORE_AGGREGATE, BOOTSTRAP_RELABEL, RELABEL_IDS, EXTRACT_DATABASE, PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON, SCORE_REPORT, MAKE_DATABASE, PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR, PLINK2_VCF, PLINK2_SCORE, SETUP_RESOURCE, PLINK2_RELABELBIM, PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE, PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:SCORE_AGGREGATE, PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM, PLINK2_MAKEBED, ANCESTRY_ANALYSIS, PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF, DOWNLOAD_SCOREFILES, PLINK2_MAKEBED_REF, RELABEL_SCOREFILE_IDS, PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES, FRAPOSA_PROJECT, MATCH_VARIANTS, PLINK2_MAKEBED_TARGET Oct-11 09:39:20.639 [main] DEBUG nextflow.Session - Igniting dataflow network (31) Oct-11 09:39:20.646 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES Oct-11 09:39:20.647 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON Oct-11 09:39:20.647 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:COMBINE_SCOREFILES Oct-11 09:39:20.647 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM Oct-11 09:39:20.648 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR Oct-11 09:39:20.648 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF Oct-11 09:39:20.648 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS Oct-11 09:39:20.649 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE Oct-11 09:39:20.649 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE Oct-11 09:39:20.649 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:SCORE_AGGREGATE Oct-11 09:39:20.655 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCALC:PGSCALC:REPORT:SCORE_REPORT Oct-11 09:39:20.656 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PGSCATALOG_PGSCALC:PGSCALC:DUMPSOFTWAREVERSIONS Oct-11 09:39:20.656 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Oct-11 09:39:20.656 [main] DEBUG nextflow.Session - Session await Oct-11 09:39:20.807 [Actor Thread 45] WARN nextflow.container.SingularityCache - Singularity cache directory has not been defined -- Remote image will be stored in the path: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location Oct-11 09:39:20.810 [Actor Thread 45] INFO nextflow.container.SingularityCache - Pulling Singularity image oras://ghcr.io/pgscatalog/pgscatalog_utils:v0.4.2-singularity [cache /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/singularity/ghcr.io-pgscatalog-pgscatalog_utils-v0.4.2-singularity.img] Oct-11 09:39:23.755 [Actor Thread 45] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=oras://ghcr.io/pgscatalog/pgscatalog_utils:v0.4.2-singularity path=/scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/singularity/ghcr.io-pgscatalog-pgscatalog_utils-v0.4.2-singularity.img Oct-11 09:39:23.847 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:23.849 [Task submitter] INFO nextflow.Session - [ef/e21346] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS002250, pgp_id:, trait_efo:]) Oct-11 09:39:23.858 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:23.858 [Task submitter] INFO nextflow.Session - [ad/1510b9] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (hgdp_tgp_samplesheet.csv) Oct-11 09:39:25.686 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (hgdp_tgp_samplesheet.csv); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/ad/1510b9f391c3aca3bc474fa88d887a] Oct-11 09:39:25.787 [Actor Thread 29] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (15) Oct-11 09:39:25.788 [Actor Thread 33] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (6) Oct-11 09:39:25.788 [Actor Thread 27] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (17) Oct-11 09:39:25.788 [Actor Thread 32] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (12) Oct-11 09:39:25.790 [Actor Thread 43] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (5) Oct-11 09:39:25.790 [Actor Thread 31] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (2) Oct-11 09:39:25.790 [Actor Thread 35] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (18) Oct-11 09:39:25.790 [Actor Thread 36] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (11) Oct-11 09:39:25.791 [Actor Thread 23] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (22) Oct-11 09:39:25.794 [Actor Thread 38] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (1) Oct-11 09:39:25.794 [Actor Thread 28] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (16) Oct-11 09:39:25.795 [Actor Thread 41] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (10) Oct-11 09:39:25.795 [Actor Thread 37] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (13) Oct-11 09:39:25.795 [Actor Thread 42] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (14) Oct-11 09:39:25.796 [Actor Thread 25] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (20) Oct-11 09:39:25.797 [Actor Thread 26] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (19) Oct-11 09:39:25.796 [Actor Thread 44] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (8) Oct-11 09:39:25.796 [Actor Thread 47] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (7) Oct-11 09:39:25.798 [Actor Thread 49] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (4) Oct-11 09:39:25.798 [Actor Thread 30] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (3) Oct-11 09:39:25.798 [Actor Thread 24] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (21) Oct-11 09:39:25.799 [Actor Thread 48] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (9) Oct-11 09:39:27.341 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS002250, pgp_id:, trait_efo:]); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/ef/e21346743c16d1510b7bdd308ee2ee] Oct-11 09:39:27.366 [Actor Thread 48] DEBUG nextflow.util.CacheHelper - Unable to get file attributes file: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/NO_FILE -- Cause: java.nio.file.NoSuchFileException: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/NO_FILE Oct-11 09:39:27.377 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:27.378 [Task submitter] INFO nextflow.Session - [d4/b36e7c] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:COMBINE_SCOREFILES (1) Oct-11 09:39:29.601 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:COMBINE_SCOREFILES (1); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/d4/b36e7cf29edc400d4f43cfe8f4bde3] Oct-11 09:39:29.674 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.675 [Task submitter] INFO nextflow.Session - [8e/daab5d] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr22) Oct-11 09:39:29.680 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.681 [Task submitter] INFO nextflow.Session - [2c/dbfb5f] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr12) Oct-11 09:39:29.686 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.686 [Task submitter] INFO nextflow.Session - [a6/15b3f3] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr3) Oct-11 09:39:29.690 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.691 [Task submitter] INFO nextflow.Session - [ab/c861c8] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr9) Oct-11 09:39:29.696 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.696 [Task submitter] INFO nextflow.Session - [3d/8cb860] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr10) Oct-11 09:39:29.702 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.702 [Task submitter] INFO nextflow.Session - [a0/22161e] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr8) Oct-11 09:39:29.710 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.710 [Task submitter] INFO nextflow.Session - [33/43378c] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr6) Oct-11 09:39:29.715 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.716 [Task submitter] INFO nextflow.Session - [94/0d3bb7] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr4) Oct-11 09:39:29.720 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.721 [Task submitter] INFO nextflow.Session - [ea/ba25c0] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr21) Oct-11 09:39:29.729 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.729 [Task submitter] INFO nextflow.Session - [e6/a764b4] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr5) Oct-11 09:39:29.736 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.752 [Task submitter] INFO nextflow.Session - [dc/118a48] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr14) Oct-11 09:39:29.760 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.761 [Task submitter] INFO nextflow.Session - [04/1ce0c0] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr16) Oct-11 09:39:29.773 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.774 [Task submitter] INFO nextflow.Session - [0d/1bb2e6] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr19) Oct-11 09:39:29.780 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.781 [Task submitter] INFO nextflow.Session - [3d/24de3c] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr17) Oct-11 09:39:29.786 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.787 [Task submitter] INFO nextflow.Session - [a1/7cd365] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr15) Oct-11 09:39:29.791 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.804 [Task submitter] INFO nextflow.Session - [58/89baa8] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr1) Oct-11 09:39:29.809 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.810 [Task submitter] INFO nextflow.Session - [4b/a3b97e] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr11) Oct-11 09:39:29.814 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.814 [Task submitter] INFO nextflow.Session - [db/2199fa] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr20) Oct-11 09:39:29.818 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.819 [Task submitter] INFO nextflow.Session - [ad/3daddd] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr7) Oct-11 09:39:29.823 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.823 [Task submitter] INFO nextflow.Session - [8c/cbc024] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr18) Oct-11 09:39:29.827 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.829 [Task submitter] INFO nextflow.Session - [b0/303f5a] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr2) Oct-11 09:39:29.833 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:29.834 [Task submitter] INFO nextflow.Session - [4d/2dea3d] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr13) Oct-11 09:39:34.940 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 46; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr22); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/8e/daab5df34e61bc2013634b0a89ead6] Oct-11 09:39:34.962 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=144; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Oct-11 09:39:35.033 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 43; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr21); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/ea/ba25c0ef8c6fe45b4e6404f868a441] Oct-11 09:39:36.760 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr20); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/db/2199fa2d0e18a1c18db8f82e765a31] Oct-11 09:39:37.108 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 45; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr19); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/0d/1bb2e6e12712e73bc7c63d0a4ea846] Oct-11 09:39:37.896 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr15); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/a1/7cd365663c22d5db7007a55e4ce4d7] Oct-11 09:39:39.067 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr18); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/8c/cbc0243e1c2c534ae8c4ae7809ac4b] Oct-11 09:39:39.125 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr14); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/dc/118a48d79a8f63bfc19b94bbd1c82c] Oct-11 09:39:39.135 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr17); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/3d/24de3c38433599c52133bb00c28b14] Oct-11 09:39:40.653 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr16); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/04/1ce0c02cb9e4a570cfb39f47fd0983] Oct-11 09:39:40.894 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr13); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/4d/2dea3d98346fb43f493bed17aeed4b] Oct-11 09:39:42.327 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 44; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr9); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/ab/c861c8fdafa50cb41c6b52e3789334] Oct-11 09:39:42.589 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr10); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/3d/8cb860fa9cd3ef258220dce363ee15] Oct-11 09:39:42.949 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr12); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/2c/dbfb5fe681e1c3951516f236f1993c] Oct-11 09:39:43.442 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr11); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/4b/a3b97ea029760aecaba33d745cf198] Oct-11 09:39:44.186 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr7); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/ad/3daddd502b4bd087fabeefc3b4f15c] Oct-11 09:39:44.621 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 42; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr8); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/a0/22161eb44c341e9e41e0ecb01a08c3] Oct-11 09:39:45.457 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 37; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr5); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/e6/a764b4cbcce8246941194726b61efd] Oct-11 09:39:45.759 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr6); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/33/43378c7c7b5fdf076561e0c20afbbe] Oct-11 09:39:47.369 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr4); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/94/0d3bb7a75e1f6f90429cbb34ba349f] Oct-11 09:39:47.983 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 47; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr3); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/a6/15b3f372a44f36e7cb4d61e05d0627] Oct-11 09:39:50.003 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr1); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/58/89baa864a88f1e642f817b9ab0e962] Oct-11 09:39:50.582 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (HgdpTgpCancerTest chromosome chr2); status: COMPLETED; exit: 0; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/b0/303f5a083b1852b20ef13c7bcfb4d6] Oct-11 09:39:50.620 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Unable to get file attributes file: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/NO_FILE -- Cause: java.nio.file.NoSuchFileException: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/NO_FILE Oct-11 09:39:50.632 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:50.632 [Task submitter] INFO nextflow.Session - [48/aa9183] Submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest) Oct-11 09:39:52.087 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 48; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest); status: COMPLETED; exit: 1; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/48/aa918313895b44b1129c01651f3ab3] Oct-11 09:39:52.089 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest); work-dir=/scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/48/aa918313895b44b1129c01651f3ab3 error [nextflow.exception.ProcessFailedException]: Process `PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest)` terminated with an error exit status (1) Oct-11 09:39:52.095 [Task monitor] INFO nextflow.processor.TaskProcessor - [48/aa9183] NOTE: Process `PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest)` terminated with an error exit status (1) -- Execution is retried (1) Oct-11 09:39:52.119 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:52.120 [Task submitter] INFO nextflow.Session - [46/75d7b4] Re-submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest) Oct-11 09:39:53.561 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 49; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest); status: COMPLETED; exit: 1; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/46/75d7b475ef5680696fe7f728405549] Oct-11 09:39:53.562 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest); work-dir=/scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/46/75d7b475ef5680696fe7f728405549 error [nextflow.exception.ProcessFailedException]: Process `PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest)` terminated with an error exit status (1) Oct-11 09:39:53.563 [Task monitor] INFO nextflow.processor.TaskProcessor - [46/75d7b4] NOTE: Process `PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest)` terminated with an error exit status (1) -- Execution is retried (2) Oct-11 09:39:53.577 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-11 09:39:53.577 [Task submitter] INFO nextflow.Session - [e7/923e73] Re-submitted process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest) Oct-11 09:39:55.014 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 50; name: PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest); status: COMPLETED; exit: 1; error: -; workDir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/e7/923e7317c475cfa41aa23837e4a396] Oct-11 09:39:55.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest); work-dir=/scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/e7/923e7317c475cfa41aa23837e4a396 error [nextflow.exception.ProcessFailedException]: Process `PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest)` terminated with an error exit status (1) Oct-11 09:39:55.029 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest)' Caused by: Process `PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest)` terminated with an error exit status (1) Command executed: export POLARS_MAX_THREADS=2 combine_matches --dataset HgdpTgpCancerTest --scorefile scorefiles.txt.gz --matches *.ipc.zst -n 2 --min_overlap 0.01 --outdir $PWD --split -v cat <<-END_VERSIONS > versions.yml MATCH_COMBINE: pgscatalog_utils: $(echo $(python -c 'import pgscatalog_utils; print(pgscatalog_utils.__version__)')) END_VERSIONS Command exit status: 1 Command output: (empty) Command error: root: 2023-10-11 09:39:54 DEBUG Verbose logging enabled pgscatalog_utils.config: 2023-10-11 09:39:54 DEBUG Using 2 threads to read CSVs pgscatalog_utils.config: 2023-10-11 09:39:54 DEBUG polars threadpool size: 2 pgscatalog_utils.match.read: 2023-10-11 09:39:54 DEBUG Reading scorefile pgscatalog_utils.match.read: 2023-10-11 09:39:54 DEBUG --chrom parameter not set, using all variants in scoring file pgscatalog_utils.match.preprocess: 2023-10-11 09:39:54 DEBUG Complementing column effect_allele pgscatalog_utils.match.preprocess: 2023-10-11 09:39:54 DEBUG Complementing column other_allele pgscatalog_utils.match.combine_matches: 2023-10-11 09:39:54 DEBUG Reading matches pgscatalog_utils.match.combine_matches: 2023-10-11 09:39:54 DEBUG Labelling match candidates pgscatalog_utils.match.label: 2023-10-11 09:39:54 DEBUG Labelling best match type (refalt > altref > ...) pgscatalog_utils.match.label: 2023-10-11 09:39:54 DEBUG Labelling duplicated best match: keeping first instance as best_match = True pgscatalog_utils.match.label: 2023-10-11 09:39:54 DEBUG Labelling multiple scoring file lines (accession/row_nr) that best_match to the same variant pgscatalog_utils.match.label: 2023-10-11 09:39:54 DEBUG Labelling all duplicates with exclude flag pgscatalog_utils.match.label: 2023-10-11 09:39:54 DEBUG Labelling ambiguous variants pgscatalog_utils.match.preprocess: 2023-10-11 09:39:54 DEBUG Complementing column REF pgscatalog_utils.match.label: 2023-10-11 09:39:54 DEBUG Labelling ambiguous variants with exclude flag pgscatalog_utils.match.label: 2023-10-11 09:39:54 DEBUG Labelling multiallelic matches with exclude flag pgscatalog_utils.match.label: 2023-10-11 09:39:54 DEBUG Not excluding flipped matches Traceback (most recent call last): File "/venv/bin/combine_matches", line 8, in sys.exit(combine_matches()) File "/venv/lib/python3.10/site-packages/pgscatalog_utils/match/combine_matches.py", line 37, in combine_matches _check_duplicate_vars(matches) File "/venv/lib/python3.10/site-packages/pgscatalog_utils/match/combine_matches.py", line 52, in _check_duplicate_vars assert max_occurrence == [1], "Duplicate IDs in final matches" AssertionError: Duplicate IDs in final matches Work dir: /scratch16/rmccoy22/abiddan1/pgs_global_cancer/pipeline/work/e7/923e7317c475cfa41aa23837e4a396 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` Oct-11 09:39:55.031 [Actor Thread 48] ERROR nextflow.Nextflow - ERROR: Matching subworkflow failed Oct-11 09:39:55.031 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (HgdpTgpCancerTest)` terminated with an error exit status (1) Oct-11 09:39:55.032 [Actor Thread 32] ERROR nextflow.Nextflow - ERROR: No scores calculated! Oct-11 09:39:55.033 [Actor Thread 47] ERROR nextflow.Nextflow - ERROR: No results report written!