The results only included fastqc and trim_galore. They seemed to be finished. The bwa dir was empty and left tasks were undone.
/*
vim: syntax=groovy
-*- mode: groovy;-*-
* -------------------------------------------------
* Nextflow config file for wanglab ChIP-seq QC
* -------------------------------------------------
* Defines reference genomes, using iGenome paths
* Imported under the default 'standard' Nextflow
* profile in nextflow.config
* I change the parameter 2017-06-07
* please see the original template
* at here:
* https://raw.githubusercontent.com/SciLifeLab/NGI-ChIPseq/master/conf/uppmax.config
*
*/
docker {
enabled = true
}
process {
container = 'scilifelab/ngi-chipseq'
executor = 'local'
cpus = 3
memory = 40G
time = 48.h
}
params {
clusterOptions = false
// illumina iGenomes reference file paths on UPPMAX
genomes {
'hg19' { bwa = '/mnt/date/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/' }
'mm10' { bwa = '/mnt/date/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/' }
'mm9' { bwa = '/mnt/date/igenomes/Mus_musculus/UCSC/mm9/Sequence/BWAIndex/' }
'GRCm38' { bwa = '/mnt/date/igenomes/Mus_musculus/NCBI/GRCm38/Sequence/BWAIndex/'}
}
}
// nextflow run SciLifeLab/NGI-ChIPseq -profile docker -c /bioware/lib/snake.config --project 'cellHeart' --reads "*.fastq" --genome GRCm38 --macsconfig 'macssetup.config'
Jun-08 14:44:04.615 [main] DEBUG nextflow.cli.Launcher - $> /bioware/bin/nextflow run SciLifeLab/NGI-ChIPseq -profile docker -c /bioware/lib/snake.config --project cellHeart --reads *.fastq --genome GRCm38 --macsconfig macssetup.config
Jun-08 14:44:04.789 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.24.1
Jun-08 14:44:05.137 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/zhenyisong/.nextflow/assets/SciLifeLab/NGI-ChIPseq/.git/config; branch: master; remote: origin; url: https://github.com/SciLifeLab/NGI-ChIPseq.git
Jun-08 14:44:05.166 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/zhenyisong/.nextflow/assets/SciLifeLab/NGI-ChIPseq/.git/config; branch: master; remote: origin; url: https://github.com/SciLifeLab/NGI-ChIPseq.git
Jun-08 14:44:05.375 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/zhenyisong/.nextflow/assets/SciLifeLab/NGI-ChIPseq/.git/config; branch: master; remote: origin; url: https://github.com/SciLifeLab/NGI-ChIPseq.git
Jun-08 14:44:05.375 [main] INFO nextflow.cli.CmdRun - Launching `SciLifeLab/NGI-ChIPseq` [sick_blackwell] - revision: c77ec52bb1 [master]
Jun-08 14:44:05.383 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/zhenyisong/.nextflow/assets/SciLifeLab/NGI-ChIPseq/nextflow.config
Jun-08 14:44:05.384 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /bioware/lib/snake.config
Jun-08 14:44:05.385 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/zhenyisong/.nextflow/assets/SciLifeLab/NGI-ChIPseq/nextflow.config
Jun-08 14:44:05.385 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /bioware/lib/snake.config
Jun-08 14:44:05.406 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'docker'
Jun-08 14:44:05.629 [main] DEBUG nextflow.Session - Session uuid: 66ae0ced-cf84-4f80-8f3f-adbd9e404e16
Jun-08 14:44:05.629 [main] DEBUG nextflow.Session - Run name: sick_blackwell
Jun-08 14:44:05.630 [main] DEBUG nextflow.Session - Executor pool size: 64
Jun-08 14:44:05.646 [main] DEBUG nextflow.cli.CmdRun -
Version: 0.24.1 build 4245
Modified: 24-03-2017 19:41 UTC (25-03-2017 03:41 CDT)
System: Linux 3.10.0-327.el7.x86_64
Runtime: Groovy 2.4.10 on OpenJDK 64-Bit Server VM 1.8.0_65-b17
Encoding: UTF-8 (UTF-8)
Process: 47303@wanglab [127.0.0.1]
CPUs: 64 - Mem: 1,007.6 GB (354 GB) - Swap: 128 GB (127.6 GB)
Jun-08 14:44:05.686 [main] DEBUG nextflow.Session - Work-dir: /mnt/date/biodata/data/cellChIP/heart/work [nfs]
Jun-08 14:44:05.974 [main] DEBUG nextflow.Session - Session start invoked
Jun-08 14:44:05.981 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
Jun-08 14:44:05.982 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
Jun-08 14:44:06.323 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-08 14:44:06.392 [main] INFO nextflow.Nextflow - ====================================
Jun-08 14:44:06.392 [main] INFO nextflow.Nextflow - ChIP-seq: v1.2
Jun-08 14:44:06.392 [main] INFO nextflow.Nextflow - ====================================
Jun-08 14:44:06.393 [main] INFO nextflow.Nextflow - Reads : *.fastq
Jun-08 14:44:06.393 [main] INFO nextflow.Nextflow - Genome : GRCm38
Jun-08 14:44:06.393 [main] INFO nextflow.Nextflow - BWA Index : /mnt/date/igenomes/Mus_musculus/NCBI/GRCm38/Sequence/BWAIndex/
Jun-08 14:44:06.393 [main] INFO nextflow.Nextflow - MACS Config : macssetup.config
Jun-08 14:44:06.393 [main] INFO nextflow.Nextflow - Extend Reads : 100 bp
Jun-08 14:44:06.394 [main] INFO nextflow.Nextflow - Current home : /home/zhenyisong
Jun-08 14:44:06.394 [main] INFO nextflow.Nextflow - Current user : zhenyisong
Jun-08 14:44:06.394 [main] INFO nextflow.Nextflow - Current path : /home/zhenyisong/biodata/data/cellChIP/heart
Jun-08 14:44:06.394 [main] INFO nextflow.Nextflow - Script dir : /home/zhenyisong/.nextflow/assets/SciLifeLab/NGI-ChIPseq
Jun-08 14:44:06.394 [main] INFO nextflow.Nextflow - Working dir : /mnt/date/biodata/data/cellChIP/heart/work
Jun-08 14:44:06.394 [main] INFO nextflow.Nextflow - Output dir : ./results
Jun-08 14:44:06.394 [main] INFO nextflow.Nextflow - Save Reference : false
Jun-08 14:44:06.394 [main] INFO nextflow.Nextflow - Save Trimmed : false
Jun-08 14:44:06.394 [main] INFO nextflow.Nextflow - Save Intermeds : false
Jun-08 14:44:06.395 [main] INFO nextflow.Nextflow - Config Profile : docker
Jun-08 14:44:06.395 [main] INFO nextflow.Nextflow - Pipeline Commit: c77ec52bb168db24d01240c164e400e84c663554
Jun-08 14:44:06.395 [main] INFO nextflow.Nextflow - ====================================
Jun-08 14:44:06.397 [main] DEBUG nextflow.Channel - files for syntax: glob; folder: ./; pattern: *.fastq; options: [:]
Jun-08 14:44:06.507 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Jun-08 14:44:06.508 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-08 14:44:06.513 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-08 14:44:06.515 [main] INFO nextflow.executor.Executor - [warm up] executor > local
Jun-08 14:44:06.519 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=64; memory=1,007.6 GB; capacity=64; pollInterval=100ms; dumpInterval=5m
Jun-08 14:44:06.522 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor
Jun-08 14:44:06.522 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jun-08 14:44:06.524 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local
Jun-08 14:44:06.548 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc)
Jun-08 14:44:06.559 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 64
Jun-08 14:44:06.574 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Jun-08 14:44:06.574 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-08 14:44:06.574 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-08 14:44:06.575 [main] DEBUG nextflow.Session - >>> barrier register (process: trim_galore)
Jun-08 14:44:06.582 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > trim_galore -- maxForks: 64
Jun-08 14:44:06.589 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <fastqc> Poison pill arrived
Jun-08 14:44:06.597 [Actor Thread 5] DEBUG nextflow.processor.StateObj - <fastqc> State before poison: StateObj[submitted: 14; completed: 0; poisoned: false ]
Jun-08 14:44:06.597 [Actor Thread 11] DEBUG nextflow.processor.TaskProcessor - <trim_galore> Poison pill arrived
Jun-08 14:44:06.598 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Jun-08 14:44:06.598 [Actor Thread 5] DEBUG nextflow.processor.StateObj - <trim_galore> State before poison: StateObj[submitted: 14; completed: 0; poisoned: false ]
Jun-08 14:44:06.598 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-08 14:44:06.598 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-08 14:44:06.599 [main] DEBUG nextflow.Session - >>> barrier register (process: bwa)
Jun-08 14:44:06.607 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bwa -- maxForks: 64
Jun-08 14:44:06.628 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Jun-08 14:44:06.629 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-08 14:44:06.629 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-08 14:44:06.631 [main] DEBUG nextflow.Session - >>> barrier register (process: samtools)
Jun-08 14:44:06.646 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > samtools -- maxForks: 64
Jun-08 14:44:06.653 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Jun-08 14:44:06.653 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-08 14:44:06.653 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-08 14:44:06.654 [main] DEBUG nextflow.Session - >>> barrier register (process: picard)
Jun-08 14:44:06.666 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > picard -- maxForks: 64
Jun-08 14:44:06.703 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Jun-08 14:44:06.703 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-08 14:44:06.703 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-08 14:44:06.704 [main] DEBUG nextflow.Session - >>> barrier register (process: countstat)
Jun-08 14:44:06.712 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > countstat -- maxForks: 64
Jun-08 14:44:06.717 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Jun-08 14:44:06.717 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-08 14:44:06.717 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-08 14:44:06.718 [main] DEBUG nextflow.Session - >>> barrier register (process: phantompeakqualtools)
Jun-08 14:44:06.725 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > phantompeakqualtools -- maxForks: 64
Jun-08 14:44:06.739 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Jun-08 14:44:06.739 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-08 14:44:06.739 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-08 14:44:06.741 [main] DEBUG nextflow.Session - >>> barrier register (process: calculateNSCRSC)
Jun-08 14:44:06.749 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > calculateNSCRSC -- maxForks: 64
Jun-08 14:44:06.755 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Jun-08 14:44:06.755 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-08 14:44:06.755 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-08 14:44:06.756 [main] DEBUG nextflow.Session - >>> barrier register (process: deepTools)
Jun-08 14:44:06.763 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > deepTools -- maxForks: 64
Jun-08 14:44:06.769 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Jun-08 14:44:06.770 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-08 14:44:06.770 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-08 14:44:06.770 [main] DEBUG nextflow.Session - >>> barrier register (process: ngsplot)
Jun-08 14:44:06.775 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > ngsplot -- maxForks: 64
Jun-08 14:44:06.779 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Jun-08 14:44:06.779 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-08 14:44:06.779 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-08 14:44:06.892 [main] DEBUG nextflow.Session - >>> barrier register (process: macs)
Jun-08 14:44:06.905 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > macs -- maxForks: 64
Jun-08 14:44:06.916 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Jun-08 14:44:06.916 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jun-08 14:44:06.917 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jun-08 14:44:06.918 [main] DEBUG nextflow.Session - >>> barrier register (process: multiqc)
Jun-08 14:44:06.927 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > multiqc -- maxForks: 64
Jun-08 14:44:06.929 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Jun-08 14:44:06.929 [main] DEBUG nextflow.Session - Session await
Jun-08 14:44:07.178 [Actor Thread 10] INFO nextflow.Session - [70/d32341] Submitted process > fastqc (SRR1029883)
Jun-08 14:44:07.202 [Actor Thread 6] INFO nextflow.Session - [a7/088a0a] Submitted process > fastqc (SRR1029879)
Jun-08 14:44:07.203 [Actor Thread 8] INFO nextflow.Session - [a0/28ff1b] Submitted process > fastqc (SRR1029881)
Jun-08 14:44:07.204 [Actor Thread 19] INFO nextflow.Session - [79/364e23] Submitted process > fastqc (SRR1029887)
Jun-08 14:44:07.205 [Actor Thread 3] INFO nextflow.Session - [65/ff76fb] Submitted process > fastqc (SRR1029878)
Jun-08 14:44:07.235 [Actor Thread 2] INFO nextflow.Session - [16/9bfa06] Submitted process > fastqc (SRR1029876)
Jun-08 14:44:07.252 [Actor Thread 15] INFO nextflow.Session - [10/bcca05] Submitted process > fastqc (SRR1029885)
Jun-08 14:44:07.253 [Actor Thread 7] INFO nextflow.Session - [d4/d037f3] Submitted process > fastqc (SRR1029880)
Jun-08 14:44:07.254 [Actor Thread 21] INFO nextflow.Session - [49/14f458] Submitted process > fastqc (SRR1029888)
Jun-08 14:44:07.255 [Actor Thread 17] INFO nextflow.Session - [84/e15b7b] Submitted process > fastqc (SRR1029886)
Jun-08 14:44:07.279 [Actor Thread 12] INFO nextflow.Session - [5d/ef5a8c] Submitted process > fastqc (SRR1029884)
Jun-08 14:44:07.279 [Actor Thread 4] INFO nextflow.Session - [77/4929ce] Submitted process > fastqc (SRR1029877)
Jun-08 14:44:07.280 [Actor Thread 23] INFO nextflow.Session - [c0/51b019] Submitted process > fastqc (SRR1029889)
Jun-08 14:44:07.281 [Actor Thread 29] INFO nextflow.Session - [08/349928] Submitted process > trim_galore (SRR1029886)
Jun-08 14:44:07.282 [Actor Thread 25] INFO nextflow.Session - [f3/0eb386] Submitted process > trim_galore (SRR1029884)
Jun-08 14:44:07.307 [Actor Thread 9] INFO nextflow.Session - [a3/ed353d] Submitted process > fastqc (SRR1029882)
Jun-08 14:44:07.310 [Actor Thread 28] INFO nextflow.Session - [ab/4d0d7a] Submitted process > trim_galore (SRR1029885)
Jun-08 14:44:07.342 [Actor Thread 26] INFO nextflow.Session - [0d/0367e1] Submitted process > trim_galore (SRR1029882)
Jun-08 14:44:07.362 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <fastqc> After stop
Jun-08 14:44:07.440 [Actor Thread 32] INFO nextflow.Session - [3c/628107] Submitted process > trim_galore (SRR1029889)
Jun-08 14:44:07.464 [Actor Thread 16] INFO nextflow.Session - [7c/257023] Submitted process > trim_galore (SRR1029877)
Jun-08 14:44:07.466 [Actor Thread 22] INFO nextflow.Session - [f9/d9551a] Submitted process > trim_galore (SRR1029880)
Jun-08 14:45:44.690 [Actor Thread 30] INFO nextflow.Session - [fa/cd80bd] Submitted process > trim_galore (SRR1029887)
Jun-08 14:45:51.804 [Actor Thread 18] INFO nextflow.Session - [65/a3aff1] Submitted process > trim_galore (SRR1029878)
Jun-08 14:46:04.052 [Actor Thread 24] INFO nextflow.Session - [cb/c95641] Submitted process > trim_galore (SRR1029881)
Jun-08 14:46:07.332 [Actor Thread 13] INFO nextflow.Session - [6a/ebf202] Submitted process > trim_galore (SRR1029876)
Jun-08 14:46:10.474 [Actor Thread 20] INFO nextflow.Session - [69/f94f3e] Submitted process > trim_galore (SRR1029879)
Jun-08 14:46:17.848 [Actor Thread 31] INFO nextflow.Session - [b0/0c5cd7] Submitted process > trim_galore (SRR1029888)
Jun-08 14:46:21.351 [Actor Thread 27] INFO nextflow.Session - [c2/5a5071] Submitted process > trim_galore (SRR1029883)
Jun-08 14:46:21.351 [Actor Thread 11] DEBUG nextflow.processor.TaskProcessor - <trim_galore> After stop
Jun-08 14:49:06.659 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 15 -- first: TaskHandler[id: 11; name: fastqc (SRR1029885); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/10/bcca05f64448dd8cc9451737dd4f52]
Jun-08 14:50:27.240 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - <fastqc> Sending poison pills and terminating process
Jun-08 14:50:27.245 [Actor Thread 39] DEBUG nextflow.Session - <<< barrier arrive (process: fastqc)
Jun-08 14:52:21.356 [Actor Thread 43] INFO nextflow.Session - [a3/d41b33] Submitted process > bwa (SRR1029877)
Jun-08 14:53:25.105 [Actor Thread 46] INFO nextflow.Session - [d6/ba338c] Submitted process > bwa (SRR1029886)
Jun-08 14:53:31.916 [Actor Thread 45] INFO nextflow.Session - [16/d2aca9] Submitted process > bwa (SRR1029884)
Jun-08 14:54:01.685 [Actor Thread 49] INFO nextflow.Session - [d0/9aa776] Submitted process > bwa (SRR1029889)
Jun-08 14:54:06.499 [Actor Thread 48] INFO nextflow.Session - [d8/c97d73] Submitted process > bwa (SRR1029876)
Jun-08 14:54:06.756 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 24; name: trim_galore (SRR1029885); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/ab/4d0d7a11574904e18ddd849fa705c1]
Jun-08 14:55:07.840 [Actor Thread 52] INFO nextflow.Session - [51/722bc2] Submitted process > bwa (SRR1029881)
Jun-08 14:56:11.801 [Actor Thread 54] INFO nextflow.Session - [a2/cdb0bc] Submitted process > bwa (SRR1029888)
Jun-08 14:56:42.878 [Actor Thread 57] INFO nextflow.Session - [5d/8d5821] Submitted process > bwa (SRR1029879)
Jun-08 14:58:15.471 [Actor Thread 60] INFO nextflow.Session - [c6/d717d2] Submitted process > bwa (SRR1029887)
Jun-08 14:58:30.396 [Actor Thread 63] INFO nextflow.Session - [27/721071] Submitted process > bwa (SRR1029878)
Jun-08 14:58:40.462 [Actor Thread 66] INFO nextflow.Session - [9e/c3922c] Submitted process > bwa (SRR1029880)
Jun-08 14:59:06.857 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 24; name: trim_galore (SRR1029885); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/ab/4d0d7a11574904e18ddd849fa705c1]
Jun-08 15:00:52.654 [Actor Thread 68] INFO nextflow.Session - [02/f85463] Submitted process > bwa (SRR1029882)
Jun-08 15:04:06.929 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 24; name: trim_galore (SRR1029885); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/ab/4d0d7a11574904e18ddd849fa705c1]
Jun-08 15:05:39.781 [Actor Thread 71] INFO nextflow.Session - [7e/89c8c5] Submitted process > bwa (SRR1029883)
Jun-08 15:09:07.027 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 24; name: trim_galore (SRR1029885); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/ab/4d0d7a11574904e18ddd849fa705c1]
Jun-08 15:13:28.526 [Actor Thread 72] DEBUG nextflow.processor.TaskProcessor - <trim_galore> Sending poison pills and terminating process
Jun-08 15:13:28.527 [Actor Thread 71] DEBUG nextflow.processor.TaskProcessor - <bwa> Poison pill arrived
Jun-08 15:13:28.527 [Actor Thread 72] DEBUG nextflow.Session - <<< barrier arrive (process: trim_galore)
Jun-08 15:13:28.529 [Actor Thread 77] DEBUG nextflow.processor.StateObj - <bwa> State before poison: StateObj[submitted: 14; completed: 0; poisoned: false ]
Jun-08 15:13:28.700 [Actor Thread 74] INFO nextflow.Session - [f1/d71c95] Submitted process > bwa (SRR1029885)
Jun-08 15:13:28.701 [Actor Thread 71] DEBUG nextflow.processor.TaskProcessor - <bwa> After stop
Jun-08 15:14:07.071 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 29; name: bwa (SRR1029877); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/a3/d41b33aae2e8f5772807af393961bd]
Jun-08 15:19:07.097 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 29; name: bwa (SRR1029877); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/a3/d41b33aae2e8f5772807af393961bd]
Jun-08 15:24:07.102 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 29; name: bwa (SRR1029877); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/a3/d41b33aae2e8f5772807af393961bd]
Jun-08 15:29:07.101 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 29; name: bwa (SRR1029877); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/a3/d41b33aae2e8f5772807af393961bd]
Jun-08 15:34:07.120 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 29; name: bwa (SRR1029877); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/a3/d41b33aae2e8f5772807af393961bd]
Jun-08 15:39:07.118 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 29; name: bwa (SRR1029877); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/a3/d41b33aae2e8f5772807af393961bd]
Jun-08 15:44:07.181 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 29; name: bwa (SRR1029877); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/a3/d41b33aae2e8f5772807af393961bd]
Jun-08 15:49:07.213 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 29; name: bwa (SRR1029877); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/a3/d41b33aae2e8f5772807af393961bd]
Jun-08 15:54:07.226 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 29; name: bwa (SRR1029877); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/a3/d41b33aae2e8f5772807af393961bd]
Jun-08 15:59:07.242 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 29; name: bwa (SRR1029877); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/a3/d41b33aae2e8f5772807af393961bd]
Jun-08 16:04:07.302 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 29; name: bwa (SRR1029877); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/a3/d41b33aae2e8f5772807af393961bd]
Jun-08 16:06:39.654 [Actor Thread 79] INFO nextflow.Session - [b6/45c4f0] Submitted process > samtools (SRR1029884)
Jun-08 16:07:18.296 [Actor Thread 82] INFO nextflow.Session - [44/8d899b] Submitted process > samtools (SRR1029876)
Jun-08 16:09:07.319 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 29; name: bwa (SRR1029877); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/a3/d41b33aae2e8f5772807af393961bd]
Jun-08 16:13:19.534 [Actor Thread 85] INFO nextflow.Session - [cd/baf6cf] Submitted process > samtools (SRR1029888)
Jun-08 16:14:07.340 [Thread-4] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 14 -- first: TaskHandler[id: 29; name: bwa (SRR1029877); status: RUNNING; exit: -; workDir: /mnt/date/biodata/data/cellChIP/heart/work/a3/d41b33aae2e8f5772807af393961bd]
Jun-08 16:16:26.939 [Actor Thread 88] INFO nextflow.Session - [87/62247c] Submitted process > picard (SRR1029876)
Jun-08 16:16:29.782 [Thread-4] ERROR nextflow.processor.TaskProcessor - Error executing process > 'picard (SRR1029876)'
Caused by:
Process `picard (SRR1029876)` terminated with an error exit status (1)
Command executed:
set -o pipefail
java -Xmx0g -jar $PICARD_HOME/picard.jar MarkDuplicates \
INPUT=SRR1029876.sorted.bam \
OUTPUT=SRR1029876.dedup.bam \
ASSUME_SORTED=true \
REMOVE_DUPLICATES=true \
METRICS_FILE=SRR1029876.picardDupMetrics.txt \
VALIDATION_STRINGENCY=LENIENT \
PROGRAM_RECORD_ID='null'
samtools sort SRR1029876.dedup.bam -o SRR1029876.dedup.sorted.bam
samtools index SRR1029876.dedup.sorted.bam
bedtools bamtobed -i SRR1029876.dedup.sorted.bam | sort -k 1,1 -k 2,2n -k 3,3n -k 6,6 > SRR1029876.dedup.sorted.bed
Command exit status:
1
Command output:
(empty)
Command error:
Invalid maximum heap size: -Xmx0g
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Work dir:
/mnt/date/biodata/data/cellChIP/heart/work/87/62247cc953c0ab6ce8db7f47800c43
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Jun-08 16:16:29.785 [Thread-4] DEBUG nextflow.Session - Session aborted -- Cause: Process `picard (SRR1029876)` terminated with an error exit status (1)
Jun-08 16:16:29.789 [main] DEBUG nextflow.Session - Session await > all process finished
Jun-08 16:16:29.789 [Actor Thread 88] DEBUG nextflow.processor.TaskProcessor - <samtools> After stop
Jun-08 16:16:29.789 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jun-08 16:16:29.789 [Actor Thread 85] DEBUG nextflow.processor.TaskProcessor - <picard> After stop
Jun-08 16:16:29.791 [Actor Thread 88] DEBUG nextflow.processor.TaskProcessor - <calculateNSCRSC> After stop
Jun-08 16:16:29.791 [Actor Thread 85] DEBUG nextflow.processor.TaskProcessor - <phantompeakqualtools> After stop
Jun-08 16:16:29.791 [Actor Thread 92] DEBUG nextflow.processor.TaskProcessor - <countstat> After stop
Jun-08 16:16:29.792 [Actor Thread 92] DEBUG nextflow.processor.TaskProcessor - <deepTools> After stop
Jun-08 16:16:29.792 [Actor Thread 88] DEBUG nextflow.processor.TaskProcessor - <macs> After stop
Jun-08 16:16:29.792 [Actor Thread 91] DEBUG nextflow.processor.TaskProcessor - <ngsplot> After stop
Jun-08 16:16:29.792 [Thread-4] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local)
Jun-08 16:16:29.792 [Actor Thread 87] DEBUG nextflow.processor.TaskProcessor - <multiqc> After stop
Jun-08 16:16:29.801 [main] WARN n.processor.TaskPollingMonitor - Killing pending tasks (13)
Jun-08 16:16:30.035 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Jun-08 16:16:30.081 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye