Dec-03 10:29:48.571 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/methylseq -profile test,docker Dec-03 10:29:48.681 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 19.10.0 Dec-03 10:29:49.160 [main] DEBUG nextflow.scm.AssetManager - Git config: /Users/katsman/.nextflow/assets/nf-core/methylseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/methylseq.git Dec-03 10:29:49.171 [main] DEBUG nextflow.scm.AssetManager - Git config: /Users/katsman/.nextflow/assets/nf-core/methylseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/methylseq.git Dec-03 10:29:49.322 [main] DEBUG nextflow.scm.AssetManager - Git config: /Users/katsman/.nextflow/assets/nf-core/methylseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/methylseq.git Dec-03 10:29:49.323 [main] INFO nextflow.cli.CmdRun - Launching `nf-core/methylseq` [tender_stonebraker] - revision: 40760ecffb [master] Dec-03 10:29:50.428 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/katsman/.nextflow/assets/nf-core/methylseq/nextflow.config Dec-03 10:29:50.428 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/katsman/.nextflow/assets/nf-core/methylseq/nextflow.config Dec-03 10:29:50.434 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker` Dec-03 10:29:51.408 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [uppmax_devel, shh_cdag, denbi_qbic, genotoul, bigpurple, uppmax, docker, gis, ccga, shh_sdag, conda, singularity, munin, prince, czbiohub_aws, hebbe, cfc, uzh, debug, test, genouest, cbe, ccga_dx, crick, czbiohub_aws_highpriority, kraken, phoenix, awsbatch, pasteur, uct_hex, aws, binac] Dec-03 10:29:51.448 [main] DEBUG nextflow.extension.OperatorEx - Dataflow extension methods: branch,buffer,chain,choice,collate,collect,collectFile,combine,concat,count,countBy,countFasta,countFastq,countLines,countText,cross,distinct,filter,first,flatMap,flatten,fork,groupBy,groupTuple,ifEmpty,into,join,last,map,max,mean,merge,min,mix,phase,print,println,randomSample,reduce,separate,set,splitCsv,splitFasta,splitFastq,splitText,spread,subscribe,sum,take,tap,toDouble,toFloat,toInteger,toList,toLong,toSortedList,transpose,unique,until,view Dec-03 10:29:51.461 [main] DEBUG nextflow.Session - Session uuid: 74f80754-04ab-467d-81ab-2b3ca033e955 Dec-03 10:29:51.462 [main] DEBUG nextflow.Session - Run name: tender_stonebraker Dec-03 10:29:51.462 [main] DEBUG nextflow.Session - Executor pool size: 16 Dec-03 10:29:51.508 [main] DEBUG nextflow.cli.CmdRun - Version: 19.10.0 build 5170 Created: 21-10-2019 15:07 UTC (18:07 IDT) System: Mac OS X 10.14.6 Runtime: Groovy 2.5.8 on OpenJDK 64-Bit Server VM 13.0.1+9 Encoding: UTF-8 (UTF-8) Process: 56691@benb-labmc3.ekmd.huji.ac.il [132.64.172.243] CPUs: 16 - Mem: 32 GB (452.7 MB) - Swap: 6 GB (1.2 GB) Dec-03 10:29:51.518 [main] DEBUG nextflow.Session - Work-dir: /Users/katsman/work [Mac OS X] Dec-03 10:29:51.540 [main] DEBUG nextflow.Session - Observer factory: TowerFactory Dec-03 10:29:51.541 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Dec-03 10:29:51.707 [main] DEBUG nextflow.Session - Session start invoked Dec-03 10:29:51.710 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /Users/katsman/results/pipeline_info/execution_trace.txt Dec-03 10:29:52.159 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Dec-03 10:29:52.266 [main] INFO nextflow.Nextflow - ---------------------------------------------------- ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/methylseq v1.4 ---------------------------------------------------- Dec-03 10:29:52.272 [main] INFO nextflow.Nextflow - Pipeline Release : master Pipeline Name : nf-core/methylseq Run Name : tender_stonebraker Reads : data/*_R{1,2}.fastq.gz Aligner : bismark Spliced alignment : No SLAM-seq : No Local alignment : No Data Type : Single-End Genome : false Fasta Ref : https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa Fasta Index : https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai Trim R1 : 0 Trim R2 : 0 Trim 3' R1 : 0 Trim 3' R2 : 0 Deduplication : Yes Directional Mode : Yes All C Contexts : No Save Reference : No Save Trimmed : No Save Unmapped : No Save Intermediates: No Current home : /Users/katsman Current path : /Users/katsman Max Resources : 6 GB memory, 2 cpus, 2d time per job Container : docker - nfcore/methylseq:1.4 Output dir : ./results Launch dir : /Users/katsman Working dir : /Users/katsman/work Script dir : /Users/katsman/.nextflow/assets/nf-core/methylseq User : katsman Config Profile : test,docker Config Description: Minimal test dataset to check pipeline function Dec-03 10:29:52.272 [main] INFO nextflow.Nextflow - ---------------------------------------------------- Dec-03 10:29:52.326 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:get_software_versions` matches process get_software_versions Dec-03 10:29:52.328 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-03 10:29:52.328 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-03 10:29:52.332 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Dec-03 10:29:52.338 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=16; memory=32 GB; capacity=16; pollInterval=100ms; dumpInterval=5m Dec-03 10:29:52.395 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > get_software_versions -- maxForks: 16 Dec-03 10:29:52.423 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:makeBismarkIndex` matches process makeBismarkIndex Dec-03 10:29:52.424 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-03 10:29:52.424 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-03 10:29:52.425 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeBismarkIndex -- maxForks: 16 Dec-03 10:29:52.438 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-03 10:29:52.439 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-03 10:29:52.440 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 16 Dec-03 10:29:52.457 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:trim_galore` matches process trim_galore Dec-03 10:29:52.458 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-03 10:29:52.458 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-03 10:29:52.460 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > trim_galore -- maxForks: 16 Dec-03 10:29:52.470 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:bismark_align` matches process bismark_align Dec-03 10:29:52.470 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-03 10:29:52.470 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-03 10:29:52.472 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bismark_align -- maxForks: 16 Dec-03 10:29:52.477 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:bismark_deduplicate` matches process bismark_deduplicate Dec-03 10:29:52.478 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-03 10:29:52.478 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-03 10:29:52.478 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bismark_deduplicate -- maxForks: 16 Dec-03 10:29:52.483 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:bismark_methXtract` matches process bismark_methXtract Dec-03 10:29:52.484 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-03 10:29:52.484 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-03 10:29:52.485 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bismark_methXtract -- maxForks: 16 Dec-03 10:29:52.500 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-03 10:29:52.500 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-03 10:29:52.501 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bismark_report -- maxForks: 16 Dec-03 10:29:52.507 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-03 10:29:52.507 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-03 10:29:52.509 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bismark_summary -- maxForks: 16 Dec-03 10:29:52.513 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:qualimap` matches process qualimap Dec-03 10:29:52.514 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-03 10:29:52.514 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-03 10:29:52.514 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > qualimap -- maxForks: 16 Dec-03 10:29:52.517 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:preseq` matches process preseq Dec-03 10:29:52.517 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-03 10:29:52.517 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-03 10:29:52.518 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > preseq -- maxForks: 16 Dec-03 10:29:52.542 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-03 10:29:52.542 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-03 10:29:52.543 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > multiqc -- maxForks: 16 Dec-03 10:29:52.555 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:29:52.559 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-03 10:29:52.559 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-03 10:29:52.559 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > output_documentation -- maxForks: 16 Dec-03 10:29:52.561 [main] DEBUG nextflow.script.BaseScript - No entry workflow defined Dec-03 10:29:52.562 [Task submitter] INFO nextflow.Session - [7e/4488bc] Submitted process > get_software_versions Dec-03 10:29:52.563 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Dec-03 10:29:52.563 [main] DEBUG nextflow.Session - Session await Dec-03 10:29:52.583 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:29:52.583 [Task submitter] INFO nextflow.Session - [4f/acbff7] Submitted process > output_documentation Dec-03 10:29:53.909 [Actor Thread 7] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=48; maxQueueSize=144; keepAlive=1m Dec-03 10:29:53.916 [FileTransfer-thread-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa at /Users/katsman/work/stage/37/8c10b92b85f0b21e190558e3dbf840/genome.fa Dec-03 10:29:53.940 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:29:53.940 [Task submitter] INFO nextflow.Session - [c1/5b3559] Submitted process > makeBismarkIndex (1) Dec-03 10:29:55.289 [FileTransfer-thread-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz at /Users/katsman/work/stage/9f/b31302f106bd7f1feb61b55485f484/SRR389222_sub1.fastq.gz Dec-03 10:29:55.301 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:29:55.302 [Task submitter] INFO nextflow.Session - [27/e97bd0] Submitted process > fastqc (SRR389222_sub1) Dec-03 10:29:55.333 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:29:55.333 [Task submitter] INFO nextflow.Session - [ec/1254a9] Submitted process > trim_galore (SRR389222_sub1) Dec-03 10:29:55.745 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: output_documentation; status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/4f/acbff7d1cc825db672f1dd4c1f545a] Dec-03 10:29:56.752 [FileTransfer-thread-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz at /Users/katsman/work/stage/e3/49b110f1c924c0614656001e398574/SRR389222_sub2.fastq.gz Dec-03 10:29:56.765 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:29:56.766 [Task submitter] INFO nextflow.Session - [5b/8d68f0] Submitted process > fastqc (SRR389222_sub2) Dec-03 10:29:57.805 [FileTransfer-thread-5] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz at /Users/katsman/work/stage/61/17f24f4cbf406e3195789537a7a553/SRR389222_sub3.fastq.gz Dec-03 10:30:03.210 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: makeBismarkIndex (1); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/c1/5b35599d3d1d397948a18246d3a635] Dec-03 10:30:03.217 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:30:03.217 [Task submitter] INFO nextflow.Session - [7e/4ae3d8] Submitted process > trim_galore (SRR389222_sub2) Dec-03 10:30:06.877 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: get_software_versions; status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/7e/4488bc20f50c09ba6532f2330003cc] Dec-03 10:30:06.882 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:30:06.882 [Task submitter] INFO nextflow.Session - [0a/493a32] Submitted process > trim_galore (SRR389222_sub3) Dec-03 10:30:11.299 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: fastqc (SRR389222_sub1); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/27/e97bd00cf6096a1781044acd5607c0] Dec-03 10:30:11.305 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:30:11.306 [Task submitter] INFO nextflow.Session - [1e/14f665] Submitted process > fastqc (SRR389222_sub3) Dec-03 10:30:11.402 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: fastqc (SRR389222_sub2); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/5b/8d68f0176cc2601b0d1523d0a69085] Dec-03 10:30:15.762 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: trim_galore (SRR389222_sub1); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/ec/1254a98756a6a078488926a2096655] Dec-03 10:30:15.809 [Actor Thread 6] DEBUG nextflow.util.CacheHelper - Unable to get file attributes file: /Users/katsman/null -- Cause: java.nio.file.NoSuchFileException: /Users/katsman/null Dec-03 10:30:15.818 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:30:15.818 [Task submitter] INFO nextflow.Session - [5e/8bd24f] Submitted process > bismark_align (SRR389222_sub1) Dec-03 10:30:21.883 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: trim_galore (SRR389222_sub2); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/7e/4ae3d860b3dd56410842a88f30d242] Dec-03 10:30:21.897 [Actor Thread 2] DEBUG nextflow.util.CacheHelper - Unable to get file attributes file: /Users/katsman/null -- Cause: java.nio.file.NoSuchFileException: /Users/katsman/null Dec-03 10:30:21.903 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:30:21.903 [Task submitter] INFO nextflow.Session - [8f/1bfc19] Submitted process > bismark_align (SRR389222_sub2) Dec-03 10:30:23.726 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: fastqc (SRR389222_sub3); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/1e/14f6651dceda6281b22feaf51c7f5f] Dec-03 10:30:27.958 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: trim_galore (SRR389222_sub3); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/0a/493a3213f8b6dbbe37d1b65bf04d96] Dec-03 10:30:27.967 [Actor Thread 6] DEBUG nextflow.util.CacheHelper - Unable to get file attributes file: /Users/katsman/null -- Cause: java.nio.file.NoSuchFileException: /Users/katsman/null Dec-03 10:30:27.973 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:30:27.974 [Task submitter] INFO nextflow.Session - [b9/a16c56] Submitted process > bismark_align (SRR389222_sub3) Dec-03 10:31:03.924 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: bismark_align (SRR389222_sub1); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/5e/8bd24f61dd26c1a2b5d22be7a7976b] Dec-03 10:31:04.008 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process bismark_align > Skipping output binding because one or more optional files are missing: fileoutparam<2> Dec-03 10:31:04.020 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:04.020 [Task submitter] INFO nextflow.Session - [4e/0f3cee] Submitted process > preseq (SRR389222_sub1) Dec-03 10:31:04.025 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:04.025 [Task submitter] INFO nextflow.Session - [f6/428fe4] Submitted process > bismark_deduplicate (SRR389222_sub1) Dec-03 10:31:07.099 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: bismark_deduplicate (SRR389222_sub1); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/f6/428fe4630e6b70b3194b938783efbe] Dec-03 10:31:07.121 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:07.122 [Task submitter] INFO nextflow.Session - [89/a311f2] Submitted process > qualimap (SRR389222_sub1) Dec-03 10:31:07.128 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:07.129 [Task submitter] INFO nextflow.Session - [03/4e9b50] Submitted process > bismark_methXtract (SRR389222_sub1) Dec-03 10:31:07.248 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: preseq (SRR389222_sub1); status: COMPLETED; exit: 139; error: -; workDir: /Users/katsman/work/4e/0f3ceefa1c7c8b5ec73a84f1dc48c0] Dec-03 10:31:07.255 [Task monitor] INFO nextflow.processor.TaskProcessor - [4e/0f3cee] NOTE: Process `preseq (SRR389222_sub1)` terminated with an error exit status (139) -- Error is ignored Dec-03 10:31:08.012 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: bismark_align (SRR389222_sub3); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/b9/a16c56d8cf2e6ba6514ec63dac5121] Dec-03 10:31:08.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process bismark_align > Skipping output binding because one or more optional files are missing: fileoutparam<2> Dec-03 10:31:08.026 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:08.026 [Task submitter] INFO nextflow.Session - [09/dd351a] Submitted process > preseq (SRR389222_sub3) Dec-03 10:31:08.030 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:08.030 [Task submitter] INFO nextflow.Session - [04/f4a2ea] Submitted process > bismark_deduplicate (SRR389222_sub3) Dec-03 10:31:11.370 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: bismark_deduplicate (SRR389222_sub3); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/04/f4a2ea6a5b1275059c4db39920cdcb] Dec-03 10:31:11.381 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:11.381 [Task submitter] INFO nextflow.Session - [a9/6906d0] Submitted process > bismark_methXtract (SRR389222_sub3) Dec-03 10:31:11.493 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: preseq (SRR389222_sub3); status: COMPLETED; exit: 1; error: -; workDir: /Users/katsman/work/09/dd351a76b5f0bf67cda4bc8972a2a9] Dec-03 10:31:11.493 [Task monitor] INFO nextflow.processor.TaskProcessor - [09/dd351a] NOTE: Process `preseq (SRR389222_sub3)` terminated with an error exit status (1) -- Error is ignored Dec-03 10:31:11.496 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:11.496 [Task submitter] INFO nextflow.Session - [1f/4aafad] Submitted process > qualimap (SRR389222_sub3) Dec-03 10:31:12.285 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: bismark_align (SRR389222_sub2); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/8f/1bfc19ea40e808bc48c3cba68cf326] Dec-03 10:31:12.288 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process bismark_align > Skipping output binding because one or more optional files are missing: fileoutparam<2> Dec-03 10:31:12.295 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:12.295 [Task submitter] INFO nextflow.Session - [b0/900543] Submitted process > bismark_deduplicate (SRR389222_sub2) Dec-03 10:31:15.408 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: qualimap (SRR389222_sub1); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/89/a311f2cc386e015c590ab08a6fd4e2] Dec-03 10:31:15.411 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:15.411 [Task submitter] INFO nextflow.Session - [4e/55ca53] Submitted process > preseq (SRR389222_sub2) Dec-03 10:31:16.288 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: bismark_deduplicate (SRR389222_sub2); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/b0/90054390a3b1dc3030b9ea2fd124b1] Dec-03 10:31:16.298 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:16.298 [Task submitter] INFO nextflow.Session - [8a/1a85cd] Submitted process > qualimap (SRR389222_sub2) Dec-03 10:31:18.941 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: preseq (SRR389222_sub2); status: COMPLETED; exit: 1; error: -; workDir: /Users/katsman/work/4e/55ca53cd8add4122627a7f047936bb] Dec-03 10:31:18.942 [Task monitor] INFO nextflow.processor.TaskProcessor - [4e/55ca53] NOTE: Process `preseq (SRR389222_sub2)` terminated with an error exit status (1) -- Error is ignored Dec-03 10:31:18.945 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:18.945 [Task submitter] INFO nextflow.Session - [09/bec8be] Submitted process > bismark_methXtract (SRR389222_sub2) Dec-03 10:31:19.720 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: qualimap (SRR389222_sub3); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/1f/4aafadf22b721f29a86a5e540ab634] Dec-03 10:31:21.402 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: bismark_methXtract (SRR389222_sub1); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/03/4e9b506d500dc655cbedfb00a2fbdb] Dec-03 10:31:21.413 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:21.413 [Task submitter] INFO nextflow.Session - [87/701cf5] Submitted process > bismark_report (SRR389222_sub1) Dec-03 10:31:23.959 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: qualimap (SRR389222_sub2); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/8a/1a85cd09bc1e8aac9f36790956bcac] Dec-03 10:31:25.408 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: bismark_report (SRR389222_sub1); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/87/701cf52550cad16046ee7813f0bd77] Dec-03 10:31:25.683 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: bismark_methXtract (SRR389222_sub3); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/a9/6906d05cea2003687bfcb98950f65d] Dec-03 10:31:25.693 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:25.693 [Task submitter] INFO nextflow.Session - [c1/c962db] Submitted process > bismark_report (SRR389222_sub3) Dec-03 10:31:29.567 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: bismark_report (SRR389222_sub3); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/c1/c962db4adc699350611629316a46e9] Dec-03 10:31:32.739 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: bismark_methXtract (SRR389222_sub2); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/09/bec8bed5431e80b10b0eeb41cef7b6] Dec-03 10:31:32.758 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:32.758 [Task submitter] INFO nextflow.Session - [16/2459ec] Submitted process > bismark_report (SRR389222_sub2) Dec-03 10:31:32.773 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:32.773 [Task submitter] INFO nextflow.Session - [7b/1a1ea9] Submitted process > bismark_summary Dec-03 10:31:36.134 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: bismark_summary; status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/7b/1a1ea9206f9e1e63670da645f0c00e] Dec-03 10:31:37.058 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: bismark_report (SRR389222_sub2); status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/16/2459ecd3190e03f0ee96038c1ecd98] Dec-03 10:31:37.091 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-03 10:31:37.092 [Task submitter] INFO nextflow.Session - [11/da283d] Submitted process > multiqc Dec-03 10:32:27.498 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: multiqc; status: COMPLETED; exit: 0; error: -; workDir: /Users/katsman/work/11/da283d6125f8e3981293c8d2e00c18] Dec-03 10:32:27.518 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'multiqc' Caused by: Missing output file(s) `*multiqc_report.html` expected by process `multiqc` Command executed: multiqc -f --config multiqc_config.yaml . \ -m custom_content -m picard -m qualimap -m bismark -m samtools -m preseq -m cutadapt -m fastqc Command exit status: 0 Command output: (empty) Command error: /opt/conda/envs/nf-core-methylseq-1.4/lib/python2.7/site-packages/multiqc/utils/config.py:45: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. configs = yaml.load(f) /opt/conda/envs/nf-core-methylseq-1.4/lib/python2.7/site-packages/multiqc/utils/config.py:51: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. sp = yaml.load(f) /opt/conda/envs/nf-core-methylseq-1.4/lib/python2.7/site-packages/multiqc/utils/config.py:121: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. new_config = yaml.load(f) [WARNING] multiqc : MultiQC Version v1.8 now available! [INFO ] multiqc : This is MultiQC v1.7 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching '.' [INFO ] multiqc : Only using modules custom_content, picard, qualimap, bismark, samtools, preseq, cutadapt, fastqc [INFO ] bismark : Found 3 bismark alignment reports [INFO ] bismark : Found 3 bismark dedup reports [INFO ] bismark : Found 3 bismark methextract reports /opt/conda/envs/nf-core-methylseq-1.4/lib/python2.7/site-packages/multiqc/modules/custom_content/custom_content.py:84: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. parsed_data = yaml.load(f['f']) [INFO ] custom_content : software_versions: Found 1 sample (html) [INFO ] custom_content : software_versions: Found 1135 samples (html) [INFO ] custom_content : nf-core-methylseq-summary: Found 1 sample (html) [INFO ] custom_content : nf-core-methylseq-summary: Found 2321 samples (html) /opt/conda/envs/nf-core-methylseq-1.4/lib/python2.7/site-packages/matplotlib/axes/_base.py:3152: UserWarning: Attempting to set identical left==right results in singular transformations; automatically expanding. left=0, right=0 'left=%s, right=%s') % (left, right)) [INFO ] qualimap : Found 3 BamQC reports [INFO ] cutadapt : Found 3 reports [INFO ] fastqc : Found 3 reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : (unreachable)/(unreachable)/multiqc_report.html [INFO ] multiqc : Data : (unreachable)/(unreachable)/multiqc_data [INFO ] multiqc : Plots : (unreachable)/(unreachable)/multiqc_plots [INFO ] multiqc : MultiQC complete Work dir: /Users/katsman/work/11/da283d6125f8e3981293c8d2e00c18 Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` Dec-03 10:32:27.534 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit Dec-03 10:32:27.534 [main] DEBUG nextflow.Session - Session await > all process finished Dec-03 10:32:27.543 [main] DEBUG nextflow.Session - Session await > all barriers passed Dec-03 10:32:27.628 [main] INFO nextflow.Nextflow - [nf-core/methylseq] Pipeline completed with errors Dec-03 10:32:27.634 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=25; failedCount=1; ignoredCount=3; cachedCount=0; succeedDuration=9m 2s; failedDuration=57.8s; cachedDuration=0ms] Dec-03 10:32:27.634 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file Dec-03 10:32:27.635 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report Dec-03 10:32:27.681 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: 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