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| Jan-23 02:39:35.355 [main] DEBUG nextflow.cli.Launcher - $> nextflow run genepi/nf-gwas -r v1.0.4 -profile test,docker | |
| Jan-23 02:39:35.404 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1 | |
| Jan-23 02:39:35.422 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/minhtoo/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected] | |
| Jan-23 02:39:35.429 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] | |
| Jan-23 02:39:35.430 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] | |
| Jan-23 02:39:35.432 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode | |
| Jan-23 02:39:35.440 [main] INFO org.pf4j.AbstractPluginManager - No plugins | |
| Jan-23 02:39:35.452 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/minhtoo/.nextflow/scm | |
| Jan-23 02:39:35.470 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] | |
| Jan-23 02:39:35.476 [main] INFO nextflow.cli.CmdRun - Pulling genepi/nf-gwas ... | |
| Jan-23 02:39:35.477 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/genepi/nf-gwas/contents/nextflow.config?ref=v1.0.4 | |
| Jan-23 02:39:36.745 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/genepi/nf-gwas/contents/main.nf?ref=v1.0.4 | |
| Jan-23 02:39:37.105 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/genepi/nf-gwas | |
| Jan-23 02:39:37.486 [main] DEBUG nextflow.scm.AssetManager - Pulling genepi/nf-gwas -- Using remote clone url: https://github.com/genepi/nf-gwas.git | |
| Jan-23 02:40:01.867 [main] INFO nextflow.cli.CmdRun - downloaded from https://github.com/genepi/nf-gwas.git | |
| Jan-23 02:40:01.890 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/nextflow.config | |
| Jan-23 02:40:01.891 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /home/minhtoo/repos/nf-gwas/nextflow.config | |
| Jan-23 02:40:01.891 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/nextflow.config | |
| Jan-23 02:40:01.891 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/minhtoo/repos/nf-gwas/nextflow.config | |
| Jan-23 02:40:01.898 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker` | |
| Jan-23 02:40:02.109 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker` | |
| Jan-23 02:40:02.228 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [slurm, development, debug, test, singularity, docker, slurm_with_scratch] | |
| Jan-23 02:40:02.260 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion | |
| Jan-23 02:40:02.261 [main] INFO nextflow.cli.CmdRun - Launching `https://github.com/genepi/nf-gwas` [grave_bardeen] DSL2 - revision: 7927c67696 [v1.0.4] | |
| Jan-23 02:40:02.263 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-validation] | |
| Jan-23 02:40:02.263 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] | |
| Jan-23 02:40:02.263 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-validation] | |
| Jan-23 02:40:02.263 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: latest | |
| Jan-23 02:40:02.777 [main] INFO nextflow.plugin.PluginUpdater - Downloading plugin [email protected] | |
| Jan-23 02:40:04.807 [main] INFO org.pf4j.util.FileUtils - Expanded plugin zip 'nf-validation-1.1.3.zip' in 'nf-validation-1.1.3' | |
| Jan-23 02:40:04.810 [main] INFO org.pf4j.AbstractPluginManager - Plugin '[email protected]' resolved | |
| Jan-23 02:40:04.811 [main] INFO org.pf4j.AbstractPluginManager - Start plugin '[email protected]' | |
| Jan-23 02:40:04.814 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started [email protected] | |
| Jan-23 02:40:04.817 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/minhtoo/.nextflow/secrets/store.json | |
| Jan-23 02:40:04.819 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@a21c74] - activable => nextflow.secret.LocalSecretsProvider@a21c74 | |
| Jan-23 02:40:04.848 [main] DEBUG nextflow.Session - Session UUID: 71b57f6d-a326-4268-8924-bd3ffcb552b9 | |
| Jan-23 02:40:04.848 [main] DEBUG nextflow.Session - Run name: grave_bardeen | |
| Jan-23 02:40:04.848 [main] DEBUG nextflow.Session - Executor pool size: 16 | |
| Jan-23 02:40:04.852 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null | |
| Jan-23 02:40:04.854 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false | |
| Jan-23 02:40:04.864 [main] DEBUG nextflow.cli.CmdRun - | |
| Version: 23.10.1 build 5891 | |
| Created: 12-01-2024 22:01 UTC (13-01-2024 06:01 SGST) | |
| System: Linux 6.5.0-14-generic | |
| Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 17.0.6+10-LTS | |
| Encoding: UTF-8 (UTF-8) | |
| Process: 63923@minhtoo [127.0.1.1] | |
| CPUs: 16 - Mem: 31.1 GB (1.6 GB) - Swap: 2 GB (7 MB) | |
| Jan-23 02:40:04.874 [main] DEBUG nextflow.Session - Work-dir: /home/minhtoo/repos/nf-gwas/work [ext2/ext3] | |
| Jan-23 02:40:04.882 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] | |
| Jan-23 02:40:04.889 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory | |
| Jan-23 02:40:04.933 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory | |
| Jan-23 02:40:04.943 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 17; maxThreads: 1000 | |
| Jan-23 02:40:05.027 [main] DEBUG nextflow.Session - Session start | |
| Jan-23 02:40:05.041 [main] DEBUG nextflow.Session - Using default localLib path: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/lib | |
| Jan-23 02:40:05.043 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/lib | |
| Jan-23 02:40:05.251 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution | |
| Jan-23 02:40:05.264 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters, paramsHelp:paramsHelp, paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-validation | |
| Jan-23 02:40:05.276 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation | |
| Jan-23 02:40:05.362 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation | |
| Jan-23 02:40:05.365 [main] INFO nextflow.Nextflow - [1mCore Nextflow options[0m | |
| [0;34mrevision : [0;32mv1.0.4[0m | |
| [0;34mrunName : [0;32mgrave_bardeen[0m | |
| [0;34mcontainerEngine : [0;32mdocker[0m | |
| [0;34mcontainer : [0;32mquay.io/genepi/nf-gwas:v1.0.4[0m | |
| [0;34mlaunchDir : [0;32m/home/minhtoo/repos/nf-gwas[0m | |
| [0;34mworkDir : [0;32m/home/minhtoo/repos/nf-gwas/work[0m | |
| [0;34mprojectDir : [0;32m/home/minhtoo/.nextflow/assets/genepi/nf-gwas[0m | |
| [0;34muserName : [0;32mminhtoo[0m | |
| [0;34mprofile : [0;32mtest,docker[0m | |
| [0;34mconfigFiles : [0;32m[0m | |
| [1mInput/output options[0m | |
| [0;34moutdir : [0;32mdefault[0m | |
| [1mAll Tests[0m | |
| [0;34mproject : [0;32mtest-gwas[0m | |
| [0;34mgenotypes_association : [0;32m/home/minhtoo/.nextflow/assets/genepi/nf-gwas/tests/input/pipeline/example.bgen[0m | |
| [0;34mgenotypes_association_format: [0;32mbgen[0m | |
| [0;34mphenotypes_filename : [0;32m/home/minhtoo/.nextflow/assets/genepi/nf-gwas/tests/input/pipeline/phenotype.txt[0m | |
| [0;34mphenotypes_columns : [0;32mY1,Y2[0m | |
| [0;34mgenotypes_prediction : [0;32m/home/minhtoo/.nextflow/assets/genepi/nf-gwas/tests/input/pipeline/example.{bim,bed,fam}[0m | |
| [1mSingle-variant tests only[0m | |
| [0;34mregenie_min_imputation_score: [0;32m0.00[0m | |
| [1mGeneral options[0m | |
| [0;34mvalidate_params : [0;32mtrue[0m | |
| [1mR report[0m | |
| [0;34mannotation_min_log10p : [0;32m2[0m | |
| [0;34mplot_ylimit : [0;32m0[0m | |
| [1mOther options[0m | |
| [0;34mgenotypes_build : [0;32mhg19[0m | |
| [0;34mrsids_filename : [0;32m/home/minhtoo/.nextflow/assets/genepi/nf-gwas/tests/input/pipeline/rsids.tsv.gz[0m | |
| !! Only displaying parameters that differ from the pipeline defaults !! | |
| -[2m----------------------------------------------------[0m- | |
| Jan-23 02:40:07.687 [main] INFO nextflow.script.BaseScript - [33mWARN: Option genotypes_build is deprecated. Please use association_build instead.[0m | |
| Jan-23 02:40:07.762 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VALIDATE_PHENOTYPES` matches process NF_GWAS:SINGLE_VARIANT_TESTS:INPUT_VALIDATION:VALIDATE_PHENOTYPES | |
| Jan-23 02:40:07.762 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:INPUT_VALIDATION:VALIDATE_PHENOTYPES | |
| Jan-23 02:40:07.763 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:INPUT_VALIDATION:VALIDATE_PHENOTYPES | |
| Jan-23 02:40:07.766 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null | |
| Jan-23 02:40:07.766 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' | |
| Jan-23 02:40:07.770 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local | |
| Jan-23 02:40:07.775 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=16; memory=31.1 GB; capacity=16; pollInterval=100ms; dumpInterval=5m | |
| Jan-23 02:40:07.776 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) | |
| Jan-23 02:40:07.823 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:QC_FILTER_GENOTYPED` matches process NF_GWAS:SINGLE_VARIANT_TESTS:QUALITY_CONTROL:QC_FILTER_GENOTYPED | |
| Jan-23 02:40:07.824 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:QUALITY_CONTROL:QC_FILTER_GENOTYPED | |
| Jan-23 02:40:07.824 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:QUALITY_CONTROL:QC_FILTER_GENOTYPED | |
| Jan-23 02:40:07.825 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null | |
| Jan-23 02:40:07.825 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' | |
| Jan-23 02:40:07.837 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:REGENIE_STEP1_RUN` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP1:REGENIE_STEP1_RUN | |
| Jan-23 02:40:07.838 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP1:REGENIE_STEP1_RUN | |
| Jan-23 02:40:07.838 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP1:REGENIE_STEP1_RUN | |
| Jan-23 02:40:07.838 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null | |
| Jan-23 02:40:07.838 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' | |
| Jan-23 02:40:07.841 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:REGENIE_LOG_PARSER_STEP1` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP1:REGENIE_LOG_PARSER_STEP1 | |
| Jan-23 02:40:07.841 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP1:REGENIE_LOG_PARSER_STEP1 | |
| Jan-23 02:40:07.841 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP1:REGENIE_LOG_PARSER_STEP1 | |
| Jan-23 02:40:07.842 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null | |
| Jan-23 02:40:07.842 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' | |
| Jan-23 02:40:07.861 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:REGENIE_STEP2_RUN` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP2:REGENIE_STEP2_RUN | |
| Jan-23 02:40:07.861 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP2:REGENIE_STEP2_RUN | |
| Jan-23 02:40:07.861 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP2:REGENIE_STEP2_RUN | |
| Jan-23 02:40:07.862 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null | |
| Jan-23 02:40:07.863 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' | |
| Jan-23 02:40:07.867 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:REGENIE_LOG_PARSER_STEP2` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP2:REGENIE_LOG_PARSER_STEP2 | |
| Jan-23 02:40:07.868 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP2:REGENIE_LOG_PARSER_STEP2 | |
| Jan-23 02:40:07.868 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP2:REGENIE_LOG_PARSER_STEP2 | |
| Jan-23 02:40:07.869 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null | |
| Jan-23 02:40:07.869 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' | |
| Jan-23 02:40:07.878 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ANNOTATE_RESULTS` matches process NF_GWAS:SINGLE_VARIANT_TESTS:ANNOTATION:ANNOTATE_RESULTS | |
| Jan-23 02:40:07.878 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:ANNOTATION:ANNOTATE_RESULTS | |
| Jan-23 02:40:07.879 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:ANNOTATION:ANNOTATE_RESULTS | |
| Jan-23 02:40:07.879 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null | |
| Jan-23 02:40:07.879 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' | |
| Jan-23 02:40:07.897 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_RESULTS` matches process NF_GWAS:SINGLE_VARIANT_TESTS:MERGE_RESULTS | |
| Jan-23 02:40:07.899 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:MERGE_RESULTS | |
| Jan-23 02:40:07.900 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:MERGE_RESULTS | |
| Jan-23 02:40:07.901 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null | |
| Jan-23 02:40:07.901 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' | |
| Jan-23 02:40:07.910 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FILTER_RESULTS` matches process NF_GWAS:SINGLE_VARIANT_TESTS:FILTER_RESULTS | |
| Jan-23 02:40:07.910 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:FILTER_RESULTS | |
| Jan-23 02:40:07.910 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:FILTER_RESULTS | |
| Jan-23 02:40:07.911 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null | |
| Jan-23 02:40:07.912 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' | |
| Jan-23 02:40:07.932 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:REPORT` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REPORTING:REPORT | |
| Jan-23 02:40:07.932 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REPORTING:REPORT | |
| Jan-23 02:40:07.932 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REPORTING:REPORT | |
| Jan-23 02:40:07.933 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null | |
| Jan-23 02:40:07.933 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' | |
| Jan-23 02:40:07.940 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:REPORT_INDEX` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REPORTING:REPORT_INDEX | |
| Jan-23 02:40:07.940 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REPORTING:REPORT_INDEX | |
| Jan-23 02:40:07.940 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NF_GWAS:SINGLE_VARIANT_TESTS:REPORTING:REPORT_INDEX | |
| Jan-23 02:40:07.941 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null | |
| Jan-23 02:40:07.941 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' | |
| Jan-23 02:40:07.943 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: COMBINE_MANIFEST_FILES, REGENIE_STEP1_SPLIT, NF_GWAS:SINGLE_VARIANT_TESTS:REPORTING:REPORT_INDEX, REGENIE_STEP1_MERGE_CHUNKS, REPORT_GENE_BASED_TESTS, FILTER_RESULTS, NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP1:REGENIE_STEP1_RUN, IMPUTED_TO_PLINK2, MERGE_RESULTS, NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP2:REGENIE_STEP2_RUN, VALIDATE_PHENOTYPES, NF_GWAS:SINGLE_VARIANT_TESTS:ANNOTATION:ANNOTATE_RESULTS, LIFTOVER_RESULTS, REGENIE_STEP1_RUN, PRUNE_GENOTYPED, CHUNK_ASSOCIATION_FILES, VALIDATE_COVARIATES, NF_GWAS:SINGLE_VARIANT_TESTS:QUALITY_CONTROL:QC_FILTER_GENOTYPED, REGENIE_LOG_PARSER_STEP1, REGENIE_LOG_PARSER_STEP2, QC_FILTER_GENOTYPED, REPORT_INDEX, REGENIE_STEP2_RUN, REPORT, DOWNLOAD_RSIDS, NF_GWAS:SINGLE_VARIANT_TESTS:MERGE_RESULTS, ANNOTATE_RESULTS, NF_GWAS:SINGLE_VARIANT_TESTS:REPORTING:REPORT, NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP1:REGENIE_LOG_PARSER_STEP1, REGENIE_STEP2_RUN_GENE_TESTS, REGENIE_STEP1_RUN_CHUNK, NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP2:REGENIE_LOG_PARSER_STEP2, NF_GWAS:SINGLE_VARIANT_TESTS:FILTER_RESULTS, NF_GWAS:SINGLE_VARIANT_TESTS:INPUT_VALIDATION:VALIDATE_PHENOTYPES | |
| Jan-23 02:40:07.946 [main] DEBUG nextflow.Session - Igniting dataflow network (23) | |
| Jan-23 02:40:07.949 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NF_GWAS:SINGLE_VARIANT_TESTS:INPUT_VALIDATION:VALIDATE_PHENOTYPES | |
| Jan-23 02:40:07.949 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/tests/input/pipeline/; pattern: example.{bim,bed,fam}; options: [checkIfExists:true] | |
| Jan-23 02:40:07.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NF_GWAS:SINGLE_VARIANT_TESTS:QUALITY_CONTROL:QC_FILTER_GENOTYPED | |
| Jan-23 02:40:07.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP1:REGENIE_STEP1_RUN | |
| Jan-23 02:40:07.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP1:REGENIE_LOG_PARSER_STEP1 | |
| Jan-23 02:40:07.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP2:REGENIE_STEP2_RUN | |
| Jan-23 02:40:07.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NF_GWAS:SINGLE_VARIANT_TESTS:REGENIE:REGENIE_STEP2:REGENIE_LOG_PARSER_STEP2 | |
| Jan-23 02:40:07.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NF_GWAS:SINGLE_VARIANT_TESTS:ANNOTATION:ANNOTATE_RESULTS | |
| Jan-23 02:40:07.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NF_GWAS:SINGLE_VARIANT_TESTS:MERGE_RESULTS | |
| Jan-23 02:40:07.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NF_GWAS:SINGLE_VARIANT_TESTS:FILTER_RESULTS | |
| Jan-23 02:40:07.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NF_GWAS:SINGLE_VARIANT_TESTS:REPORTING:REPORT | |
| Jan-23 02:40:07.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NF_GWAS:SINGLE_VARIANT_TESTS:REPORTING:REPORT_INDEX | |
| Jan-23 02:40:07.951 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: | |
| Script_da7a07aef5313a71: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././../modules/local/chunking/combine_manifest_files.nf | |
| Script_c397dfbab89b1c8f: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/nf_gwas.nf | |
| Script_15a59546ef65518e: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././regenie/./../../modules/local/regenie/regenie_log_parser_step1.nf | |
| Script_efd4c9941fd49b22: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././regenie/./../../modules/local/regenie/regenie_step1_run.nf | |
| Script_e5d7a166132484b0: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././regenie/./../../modules/local/regenie/regenie_step2_run.nf | |
| Script_ea8a750cbb3524c0: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././../modules/local/chunking/chunk_association_files.nf | |
| Script_5a8cd2731c1816ea: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././regenie/./regenie_step2.nf | |
| Script_16172314a3090d3a: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././pruning.nf | |
| Script_24d056d1594eb4fd: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/main.nf | |
| Script_2a29f773dd02c57a: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/./../modules/local/merge_results.nf | |
| Script_9e383825f3c088c9: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././annotation.nf | |
| Script_a5652591944dc8f6: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/./single_variant_tests.nf | |
| Script_077d9c3c617d7bea: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././regenie/./../../modules/local/regenie/regenie_log_parser_step2.nf | |
| Script_a99eeb03167b6384: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././quality_control.nf | |
| Script_f50d260e0ee0c4f1: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././reporting.nf | |
| Script_03143ee59f92cbc6: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././../modules/local/reporting/report_index.nf | |
| Script_67d0694fd6cbf130: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././../modules/local/input_validation/validate_phenotypes.nf | |
| Script_9f03932fd1835566: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/./gene_based_tests.nf | |
| Script_30dc6fbc8bc2c1ef: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/./../modules/local/filter_results.nf | |
| Script_b5be466539a5ccf5: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/./../modules/local/imputed_to_plink2.nf | |
| Script_0cd50b096919322b: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././../modules/local/reporting/report.nf | |
| Script_daa54123b5542f3f: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././input_validation.nf | |
| Script_ca34108566b84243: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././regenie/regenie.nf | |
| Script_e9c74727b33157ba: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././lift_over.nf | |
| Script_5568f8a32a31050c: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././../modules/local/qc_filter_genotyped.nf | |
| Script_580a352169d4f867: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././../modules/local/input_validation/validate_covariates.nf | |
| Script_2a45b084e3108863: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././../modules/local/annotation/annotate_results.nf | |
| Script_21bfc4473751b6e7: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././regenie/./../../modules/local/regenie/regenie_step1_run_chunk.nf | |
| Script_ae571c08e6824aad: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././regenie/./../../modules/local/regenie/regenie_step2_run_gene_tests.nf | |
| Script_ff1c7c02569edf47: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././../modules/local/liftover_results.nf | |
| Script_de68d875ad831b83: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././regenie/./regenie_step1.nf | |
| Script_c4da5ceb8494b2a9: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././../modules/local/prune_genotyped.nf | |
| Script_3f81133ee3eb671c: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././../modules/local/annotation/download_rsids.nf | |
| Script_a98ca5ce563a5d84: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././reporting_gene_tests.nf | |
| Script_d4184e7637610c58: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././../modules/local/reporting/report_gene_based_tests.nf | |
| Script_7736ef805c830722: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././chunking.nf | |
| Script_20af96a83339d673: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././regenie/./../../modules/local/regenie/regenie_step1_split.nf | |
| Script_fbe5f4016af3cb65: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././regenie/./../../modules/local/regenie/regenie_step1_merge_chunks.nf | |
| Script_0d452ccfd36c1c7d: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/./workflows/././regenie/./regenie_step2_gene_tests.nf | |
| Jan-23 02:40:07.951 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination | |
| Jan-23 02:40:07.951 [main] DEBUG nextflow.Session - Session await | |
| Jan-23 02:40:08.006 [Actor Thread 12] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/tests/input/pipeline/phenotype.txt | |
| Jan-23 02:40:08.014 [Actor Thread 6] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/tests/input/pipeline/example.bed | |
| Jan-23 02:40:08.014 [Actor Thread 6] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/tests/input/pipeline/example.bim | |
| Jan-23 02:40:08.014 [Actor Thread 6] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/minhtoo/.nextflow/assets/genepi/nf-gwas/tests/input/pipeline/example.fam | |
| Jan-23 02:40:08.053 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Jan-23 02:40:08.055 [Task submitter] INFO nextflow.Session - [e1/93c623] Submitted process > NF_GWAS:SINGLE_VARIANT_TESTS:QUALITY_CONTROL:QC_FILTER_GENOTYPED (1) | |
| Jan-23 02:40:08.061 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Jan-23 02:40:08.061 [Task submitter] INFO nextflow.Session - [67/2c9d8b] Submitted process > NF_GWAS:SINGLE_VARIANT_TESTS:INPUT_VALIDATION:VALIDATE_PHENOTYPES | |
| Jan-23 02:45:07.915 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- submitted tasks are shown below | |
| ~> TaskHandler[id: 2; name: NF_GWAS:SINGLE_VARIANT_TESTS:QUALITY_CONTROL:QC_FILTER_GENOTYPED (1); status: RUNNING; exit: -; error: -; workDir: /home/minhtoo/repos/nf-gwas/work/e1/93c6238c11c0659e5b90902261c4e1] | |
| ~> TaskHandler[id: 1; name: NF_GWAS:SINGLE_VARIANT_TESTS:INPUT_VALIDATION:VALIDATE_PHENOTYPES; status: RUNNING; exit: -; error: -; workDir: /home/minhtoo/repos/nf-gwas/work/67/2c9d8bb4fc32697ff0dc958459cc42] |
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