Oct-27 08:34:11.521 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/eager -r dev -profile docker --input '/mnt/h/PRJEB36983maxplanck/ERR4300305_*{1,2}.fastq.gz' --mapper bowtie2 --bt2_index /home/teemu/dna --fasta /home/teemu/dna/hs37d5.fa --outdir /home/teemu/muumio/kra11c -w /home/teemu/eagerulko5 Oct-27 08:34:11.621 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 20.07.1 Oct-27 08:34:12.164 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/teemu/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git Oct-27 08:34:12.174 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/teemu/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git Oct-27 08:34:12.372 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/teemu/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git Oct-27 08:34:12.372 [main] INFO nextflow.cli.CmdRun - Launching `nf-core/eager` [peaceful_liskov] - revision: f2a326d1b1 [dev] Oct-27 08:34:13.193 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/teemu/.nextflow/assets/nf-core/eager/nextflow.config Oct-27 08:34:13.194 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/teemu/.nextflow/assets/nf-core/eager/nextflow.config Oct-27 08:34:13.200 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker` Oct-27 08:34:14.297 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [test_tsv, test_tsv_fna, cfc_dev, denbi_qbic, genotoul, uppmax, abims, benchmarking_human, mpcdf, test_tsv_kraken, czbiohub_aws, ccga_med, test, google, kraken, shh, pasteur, test_fna, bi, bigpurple, test_pretrim, test_bam, docker, gis, benchmarking_vikingfish, utd_ganymede, test_humanbam, conda, singularity, icr_davros, test_tsv_humanbam, test_kraken, munin, prince, hebbe, cfc, uzh, debug, genouest, cbe, ebc, ccga_dx, test_tsv_pretrim, crick, test_tsv_complex, phoenix, awsbatch, uct_hpc, test_tsv_bam, binac] Oct-27 08:34:14.339 [main] DEBUG nextflow.Session - Session uuid: dc9bc4f6-3871-432e-8d33-336e8c8e56e9 Oct-27 08:34:14.339 [main] DEBUG nextflow.Session - Run name: peaceful_liskov Oct-27 08:34:14.340 [main] DEBUG nextflow.Session - Executor pool size: 24 Oct-27 08:34:14.360 [main] DEBUG nextflow.cli.CmdRun - Version: 20.07.1 build 5412 Created: 24-07-2020 15:18 UTC (18:18 EEST) System: Linux 5.4.51-microsoft-standard-WSL2-dx Runtime: Groovy 2.5.11 on OpenJDK 64-Bit Server VM 11.0.8+10-post-Ubuntu-0ubuntu120.04 Encoding: UTF-8 (UTF-8) Process: 32427@DESKTOP-HB9O8BS [127.0.1.1] CPUs: 24 - Mem: 41.2 GB (22.2 GB) - Swap: 150 GB (150 GB) Oct-27 08:34:14.373 [main] DEBUG nextflow.Session - Work-dir: /home/teemu/eagerulko5 [ext2/ext3] Oct-27 08:34:14.401 [main] DEBUG nextflow.Session - Observer factory: TowerFactory Oct-27 08:34:14.403 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Oct-27 08:34:14.571 [main] DEBUG nextflow.Session - Session start invoked Oct-27 08:34:14.575 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/teemu/muumio/kra11c/pipeline_info/execution_trace.txt Oct-27 08:34:15.902 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Oct-27 08:34:15.916 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: library_merge, genotyping_hc, output_documentation, eigenstrat_snp_coverage, nuclear_contamination, makeFastaIndex, convertBam, multivcfanalyzer, mtnucratio, genotyping_freebayes, lanemerge_hostremoval_fastq, hostremoval_input_fastq, makeSeqDict, genotyping_ug, makeBT2Index, bowtie2, adapter_removal, maltextract, bwa, malt, genotyping_angsd, kraken, vcf2genome, samtools_flagstat, unzip_reference, sex_deterrmine, bedtools, damageprofiler, seqtype_merge, fastqc_after_clipping, circularmapper, preseq, genotyping_pileupcaller, kraken_parse, samtools_flagstat_after_filter, indexinputbam, bam_trim, samtools_filter, print_nuclear_contamination, get_software_versions, bwamem, additional_library_merge, circulargenerator, multiqc, fastp, endorSpy, qualimap, kraken_merge, decomp_kraken, lanemerge, dedup, pmdtools, fastqc, makeBWAIndex, markduplicates Oct-27 08:34:16.109 [main] INFO nextflow.Nextflow - Oct-27 08:34:16.111 [main] INFO nextflow.Nextflow - No TSV file provided - creating TSV from supplied directory. Oct-27 08:34:16.112 [main] INFO nextflow.Nextflow - Reading path(s): /mnt/h/PRJEB36983maxplanck/ERR4300305_*{1,2}.fastq.gz Oct-27 08:34:16.113 [main] INFO nextflow.Nextflow - Generating paired-end FASTQ data TSV Oct-27 08:34:16.114 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /mnt/h/PRJEB36983maxplanck/; pattern: ERR4300305_*{1,2}.fastq.gz; options: [:] Oct-27 08:34:16.204 [main] INFO nextflow.Nextflow - ---------------------------------------------------- ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/eager v2.3.0dev ---------------------------------------------------- Oct-27 08:34:16.207 [main] INFO nextflow.Nextflow - Pipeline Name : nf-core/eager Pipeline Version : 2.3.0dev Pipeline Release : dev Run Name : peaceful_liskov Input : /mnt/h/PRJEB36983maxplanck/ERR4300305_*{1,2}.fastq.gz Convert input BAM?: No Fasta Ref : /home/teemu/dna/hs37d5.fa BAM Index Type : CSI BWA Index : Yes Skipping FASTQC? : No Skipping AdapterRemoval?: No Skip Read Merging : No Skip Adapter Trimming: No Running BAM filtering: No Run Fastq Host Removal: No Skipping Preseq? : No Skipping Deduplication?: No Skipping DamageProfiler?: No Skipping Qualimap?: No Run BAM Trimming? : No Run PMDtools? : No Run Genotyping? : No Run MultiVCFAnalyzer: No Run VCF2Genome : No Run SexDetErrMine : No Run Nuclear Contamination Estimation: No Run Bedtools Coverage: No Run Metagenomic Binning: No Max Resources : 128 GB memory, 16 cpus, 10d time per job Output Dir : /home/teemu/muumio/kra11c Working Dir : /home/teemu/eagerulko5 Container Engine : docker Container : nfcore/eager:dev Current Home : /home/teemu Current User : teemu Script Dir : /home/teemu/.nextflow/assets/nf-core/eager Config Profile : docker User : teemu Oct-27 08:34:16.208 [main] INFO nextflow.Nextflow - ---------------------------------------------------- Oct-27 08:34:16.266 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:sc_small` matches label `sc_small` for process with name makeFastaIndex Oct-27 08:34:16.267 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-27 08:34:16.267 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-27 08:34:16.270 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Oct-27 08:34:16.274 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=24; memory=41.2 GB; capacity=24; pollInterval=100ms; dumpInterval=5m Oct-27 08:34:16.338 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:sc_medium` matches label `sc_medium` for process with name makeSeqDict Oct-27 08:34:16.339 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-27 08:34:16.340 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-27 08:34:16.398 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mc_small` matches label `mc_small` for process with name convertBam Oct-27 08:34:16.399 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-27 08:34:16.399 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-27 08:34:16.430 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:sc_small` matches label `sc_small` for process with name indexinputbam Oct-27 08:34:16.430 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-27 08:34:16.430 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-27 08:34:16.443 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:sc_small` matches label `sc_small` for process with name fastqc Oct-27 08:34:16.443 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-27 08:34:16.443 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-27 08:34:16.453 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mc_small` matches label `mc_small` for process with name fastp Oct-27 08:34:16.454 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-27 08:34:16.454 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-27 08:34:16.469 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mc_small` matches label `mc_small` for process with name adapter_removal Oct-27 08:34:16.470 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-27 08:34:16.470 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-27 08:34:16.501 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:sc_tiny` matches label `sc_tiny` for process with name lanemerge Oct-27 08:34:16.502 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-27 08:34:16.502 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-27 08:34:16.519 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:sc_tiny` matches label `sc_tiny` for process with name lanemerge_hostremoval_fastq Oct-27 08:34:16.520 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-27 08:34:16.520 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-27 08:34:16.526 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:sc_small` matches label `sc_small` for process with name fastqc_after_clipping Oct-27 08:34:16.527 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-27 08:34:16.527 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-27 08:34:16.536 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mc_medium` matches label `mc_medium` for process with name bwa Oct-27 08:34:16.536 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-27 08:34:16.536 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-27 08:34:16.540 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-27 08:34:16.541 [main] DEBUG nextflow.Session - Session aborted -- Cause: Unknown variable 'bwa_index_bwamem' Oct-27 08:34:16.548 [Task submitter] INFO nextflow.Session - [11/509de8] Submitted process > makeSeqDict (hs37d5.fa) Oct-27 08:34:16.572 [main] DEBUG nextflow.Session - The following nodes are still active: [process] lanemerge status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] fastqc_after_clipping status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ Oct-27 08:34:16.596 [main] ERROR nextflow.cli.Launcher - @unknown groovy.lang.MissingPropertyException: Unknown variable 'bwa_index_bwamem' at jdk.internal.reflect.GeneratedConstructorAccessor66.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:80) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:74) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:265) at nextflow.script.ProcessConfig.getProperty(ProcessConfig.groovy:273) at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:190) at groovy.lang.Closure.getPropertyTryThese(Closure.java:313) at groovy.lang.Closure.getPropertyDelegateFirst(Closure.java:303) at groovy.lang.Closure.getProperty(Closure.java:288) at org.codehaus.groovy.runtime.callsite.PogoGetPropertySite.getProperty(PogoGetPropertySite.java:49) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:309) at Script_502473b1$_runScript_closure86.doCall(Script_502473b1:1518) at Script_502473b1$_runScript_closure86.doCall(Script_502473b1) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:101) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041) at groovy.lang.Closure.call(Closure.java:405) at groovy.lang.Closure.call(Closure.java:399) at nextflow.script.ProcessFactory.createProcessor(ProcessFactory.groovy:95) at nextflow.script.ProcessFactory$createProcessor.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at nextflow.script.ProcessFactory$createProcessor.call(Unknown Source) at nextflow.script.BaseScript.process(BaseScript.groovy:115) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176) at Script_502473b1.runScript(Script_502473b1:1511) at nextflow.script.BaseScript.runDsl1(BaseScript.groovy:164) at nextflow.script.BaseScript.run(BaseScript.groovy:200) at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:219) at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:219) at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:127) at nextflow.cli.CmdRun.run(CmdRun.groovy:274) at nextflow.cli.Launcher.run(Launcher.groovy:466) at nextflow.cli.Launcher.main(Launcher.groovy:648)