ERROR ~ Execution aborted due to an unexpected error

[Carlos Guzman]

Testing an R script for differential gene expression analysis. The DGE completes successfully, but then this error appears and the downstream analysis is aborted.

ERROR ~ Execution aborted due to an unexpected error

The error says I should look at the nextflow.log, but honestly i'm not even sure what i'm reading.

I'd appreciate any help.

Jan-24 10:15:57.372 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: [proxy.swmed.edu, 3128]
Jan-24 10:15:57.483 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: [proxy.swmed.edu, 3128]
Jan-24 10:15:57.483 [main] DEBUG nextflow.cli.Launcher - $> /usr/local/anaconda2/bin/nextflow run /dataB/code/nextflow-pipe/main.nf --mode rna --config /dataB/projects/test_projects/all_config.txt --fasta /dataA/data/hg19_gencode/GRCh37.p13.genome.fa --gtf /dataA/data/hg19_gencode/gencode.v19.annotation.gtf --library PE --genome hg19 --threads 10 --subsample --experiment /dataB/projects/test_projects/experiment.txt
Jan-24 10:15:57.603 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 0.23.0
Jan-24 10:15:57.676 [main] INFO  nextflow.cli.CmdRun - Launching `/dataB/code/nextflow-pipe/main.nf` [infallible_mcnulty] - revision: 0919131d98
Jan-24 10:15:57.682 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /dataB/code/nextflow-pipe/nextflow.config
Jan-24 10:15:57.684 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /dataB/code/nextflow-pipe/nextflow.config
Jan-24 10:15:58.085 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'standard'
Jan-24 10:15:58.145 [main] DEBUG nextflow.Session - Session uuid: 249411c1-d8ac-4822-81be-605535e0727f
Jan-24 10:15:58.146 [main] DEBUG nextflow.Session - Run name: infallible_mcnulty
Jan-24 10:15:58.146 [main] DEBUG nextflow.Session - Executor pool size: 32
Jan-24 10:15:58.157 [main] DEBUG nextflow.cli.CmdRun -
  Version: 0.23.0 build 4139
  Modified: 13-12-2016 14:24 UTC (08:24 CDT)
  System: Linux 3.19.0-64-generic
  Runtime: Groovy 2.4.7 on OpenJDK 64-Bit Server VM 1.7.0_91-b15
  Encoding: UTF-8 (UTF-8)
  Process: 2054@ubuntu1404 [127.0.1.1]
  CPUs: 32 - Mem: 125.8 GB (34.3 GB) - Swap: 32 GB (31 GB)
Jan-24 10:15:58.169 [main] DEBUG nextflow.Session - Work-dir: /dataB/projects/test_projects/work [xfs]
Jan-24 10:15:58.323 [main] DEBUG nextflow.Session - Session start invoked
Jan-24 10:15:58.330 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
Jan-24 10:15:58.331 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
Jan-24 10:15:59.595 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jan-24 10:15:59.618 [main] INFO  nextflow.Nextflow -
Jan-24 10:15:59.618 [main] INFO  nextflow.Nextflow - ~ version 1.0.0
Jan-24 10:15:59.618 [main] INFO  nextflow.Nextflow - ========================================
Jan-24 10:15:59.618 [main] INFO  nextflow.Nextflow - mode:       rna
Jan-24 10:15:59.619 [main] INFO  nextflow.Nextflow - config:     /dataB/projects/test_projects/all_config.txt
Jan-24 10:15:59.619 [main] INFO  nextflow.Nextflow - FASTA:      /dataA/data/hg19_gencode/GRCh37.p13.genome.fa
Jan-24 10:15:59.619 [main] INFO  nextflow.Nextflow - GTF:        /dataA/data/hg19_gencode/gencode.v19.annotation.gtf
Jan-24 10:15:59.619 [main] INFO  nextflow.Nextflow - library:    PE
Jan-24 10:15:59.619 [main] INFO  nextflow.Nextflow - genome:     hg19
Jan-24 10:15:59.619 [main] INFO  nextflow.Nextflow - threads:    10
Jan-24 10:15:59.619 [main] INFO  nextflow.Nextflow - macs-size:  2792200507
Jan-24 10:15:59.619 [main] INFO  nextflow.Nextflow - epic-size:  hg19
Jan-24 10:15:59.619 [main] INFO  nextflow.Nextflow - qvalue:     0.01
Jan-24 10:15:59.620 [main] INFO  nextflow.Nextflow -
Jan-24 10:15:59.620 [main] INFO  nextflow.Nextflow - subsample:  true
Jan-24 10:15:59.620 [main] INFO  nextflow.Nextflow - ========================================
Jan-24 10:15:59.620 [main] INFO  nextflow.Nextflow -
Jan-24 10:15:59.768 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jan-24 10:15:59.768 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jan-24 10:15:59.775 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jan-24 10:15:59.777 [main] INFO  nextflow.executor.Executor - [warm up] executor > local
Jan-24 10:15:59.780 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=32; memory=125.8 GB; capacity=32; pollInterval=100ms; dumpInterval=5m
Jan-24 10:15:59.784 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor
Jan-24 10:15:59.785 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jan-24 10:15:59.786 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local
Jan-24 10:15:59.818 [main] DEBUG nextflow.Session - >>> barrier register (process: subsample_reads)
Jan-24 10:15:59.827 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > subsample_reads -- maxForks: 32
Jan-24 10:15:59.855 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <subsample_reads> Poison pill arrived
Jan-24 10:15:59.857 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jan-24 10:15:59.857 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jan-24 10:15:59.857 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jan-24 10:15:59.857 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <subsample_reads> State before poison: StateObj[submitted: 6; completed: 0; poisoned: false ]
Jan-24 10:15:59.859 [main] DEBUG nextflow.Session - >>> barrier register (process: fetchChromSizes)
Jan-24 10:15:59.866 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fetchChromSizes -- maxForks: 32
Jan-24 10:15:59.870 [Actor Thread 9] DEBUG nextflow.processor.TaskProcessor - <fetchChromSizes> Poison pill arrived
Jan-24 10:15:59.871 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <fetchChromSizes> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
Jan-24 10:15:59.871 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jan-24 10:15:59.872 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jan-24 10:15:59.872 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jan-24 10:15:59.872 [main] DEBUG nextflow.Session - >>> barrier register (process: trimming)
Jan-24 10:15:59.879 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > trimming -- maxForks: 32
Jan-24 10:15:59.884 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jan-24 10:15:59.884 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jan-24 10:15:59.885 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jan-24 10:15:59.885 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc)
Jan-24 10:15:59.892 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 32
Jan-24 10:15:59.899 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jan-24 10:15:59.899 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jan-24 10:15:59.899 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jan-24 10:15:59.900 [main] DEBUG nextflow.Session - >>> barrier register (process: mapping)
Jan-24 10:15:59.907 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > mapping -- maxForks: 32
Jan-24 10:15:59.915 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jan-24 10:15:59.915 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jan-24 10:15:59.915 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jan-24 10:15:59.916 [main] DEBUG nextflow.Session - >>> barrier register (process: qc_metrics)
Jan-24 10:15:59.922 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > qc_metrics -- maxForks: 32
Jan-24 10:15:59.927 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jan-24 10:15:59.927 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jan-24 10:15:59.927 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jan-24 10:15:59.928 [main] DEBUG nextflow.Session - >>> barrier register (process: preseq)
Jan-24 10:15:59.936 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > preseq -- maxForks: 32
Jan-24 10:15:59.941 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jan-24 10:15:59.941 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jan-24 10:15:59.942 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jan-24 10:15:59.942 [main] DEBUG nextflow.Session - >>> barrier register (process: featureCounts)
Jan-24 10:15:59.950 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > featureCounts -- maxForks: 32
Jan-24 10:15:59.960 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jan-24 10:15:59.960 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jan-24 10:15:59.960 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jan-24 10:15:59.961 [main] DEBUG nextflow.Session - >>> barrier register (process: stringTie)
Jan-24 10:15:59.969 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > stringTie -- maxForks: 32
Jan-24 10:15:59.986 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jan-24 10:15:59.986 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jan-24 10:15:59.986 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jan-24 10:15:59.988 [main] DEBUG nextflow.Session - >>> barrier register (process: dge)
Jan-24 10:15:59.996 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > dge -- maxForks: 32
Jan-24 10:16:00.011 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Jan-24 10:16:00.011 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Jan-24 10:16:00.012 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Jan-24 10:16:00.012 [main] DEBUG nextflow.Session - >>> barrier register (process: multiqc)
Jan-24 10:16:00.021 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > multiqc -- maxForks: 32
Jan-24 10:16:00.024 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Jan-24 10:16:00.024 [main] DEBUG nextflow.Session - Session await
Jan-24 10:16:00.070 [Actor Thread 3] INFO  nextflow.Session - [2e/fe4959] Submitted process > subsample_reads (1)
Jan-24 10:16:00.070 [Actor Thread 10] INFO  nextflow.Session - [6d/9e39de] Submitted process > fetchChromSizes (1)
Jan-24 10:16:00.071 [Actor Thread 4] INFO  nextflow.Session - [b5/22e72d] Submitted process > subsample_reads (2)
Jan-24 10:16:00.072 [Actor Thread 5] INFO  nextflow.Session - [ba/34d819] Submitted process > subsample_reads (3)
Jan-24 10:16:00.072 [Actor Thread 8] INFO  nextflow.Session - [a8/b70491] Submitted process > subsample_reads (6)
Jan-24 10:16:00.072 [Actor Thread 9] DEBUG nextflow.processor.TaskProcessor - <fetchChromSizes> After stop
Jan-24 10:16:00.073 [Actor Thread 6] INFO  nextflow.Session - [3b/31f107] Submitted process > subsample_reads (4)
Jan-24 10:16:00.074 [Actor Thread 7] INFO  nextflow.Session - [3d/da61e4] Submitted process > subsample_reads (5)
Jan-24 10:16:00.074 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - <subsample_reads> After stop
Jan-24 10:16:10.878 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - <fetchChromSizes> Sending poison pills and terminating process
Jan-24 10:16:10.880 [Actor Thread 2] DEBUG nextflow.Session - <<< barrier arrive (process: fetchChromSizes)
Jan-24 10:20:59.993 [Thread-1] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- first: TaskHandler[id: 1; name: subsample_reads (1); status: RUNNING; exit: -; workDir: /dataB/projects/test_projects/work/2e/fe4959b17132f079e884e976a2f76b]
Jan-24 10:24:44.347 [Actor Thread 1] INFO  nextflow.Session - [59/5e3525] Submitted process > trimming (1)
Jan-24 10:24:45.510 [Actor Thread 16] INFO  nextflow.Session - [08/dae6b3] Submitted process > fastqc (1)
Jan-24 10:24:45.526 [Actor Thread 1] INFO  nextflow.Session - [85/0f5d10] Submitted process > mapping (1)
Jan-24 10:26:00.016 [Thread-1] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- first: TaskHandler[id: 1; name: subsample_reads (1); status: RUNNING; exit: -; workDir: /dataB/projects/test_projects/work/2e/fe4959b17132f079e884e976a2f76b]
Jan-24 10:26:38.533 [Actor Thread 16] INFO  nextflow.Session - [75/821edf] Submitted process > trimming (2)
Jan-24 10:26:40.766 [Actor Thread 19] INFO  nextflow.Session - [39/26956b] Submitted process > fastqc (2)
Jan-24 10:26:40.773 [Actor Thread 20] INFO  nextflow.Session - [aa/689451] Submitted process > mapping (2)
Jan-24 10:27:58.777 [Actor Thread 19] DEBUG nextflow.processor.TaskProcessor - <qc_metrics> Poison pill arrived
Jan-24 10:27:58.778 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <qc_metrics> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
Jan-24 10:27:58.788 [Actor Thread 22] INFO  nextflow.Session - [1e/059f98] Submitted process > qc_metrics (1)
Jan-24 10:27:58.789 [Actor Thread 19] DEBUG nextflow.processor.TaskProcessor - <qc_metrics> After stop
Jan-24 10:27:58.789 [Actor Thread 25] INFO  nextflow.Session - [13/811fa1] Submitted process > featureCounts (1)
Jan-24 10:27:58.807 [Actor Thread 26] INFO  nextflow.Session - [f5/9677d6] Submitted process > preseq (1)
Jan-24 10:27:58.807 [Actor Thread 21] INFO  nextflow.Session - [d1/7713f7] Submitted process > stringTie (1)
Jan-24 10:29:36.647 [Actor Thread 31] INFO  nextflow.Session - [43/baa1d1] Submitted process > trimming (3)
Jan-24 10:29:39.243 [Actor Thread 36] INFO  nextflow.Session - [3d/2b3cad] Submitted process > fastqc (3)
Jan-24 10:29:39.245 [Actor Thread 35] INFO  nextflow.Session - [6d/d3fade] Submitted process > mapping (3)
Jan-24 10:30:56.687 [Actor Thread 37] INFO  nextflow.Session - [e8/f6788a] Submitted process > stringTie (2)
Jan-24 10:30:56.688 [Actor Thread 39] INFO  nextflow.Session - [ab/7f7048] Submitted process > preseq (2)
Jan-24 10:30:56.695 [Actor Thread 36] INFO  nextflow.Session - [f8/567529] Submitted process > featureCounts (2)
Jan-24 10:31:00.087 [Thread-1] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 8 -- first: TaskHandler[id: 6; name: subsample_reads (6); status: RUNNING; exit: -; workDir: /dataB/projects/test_projects/work/a8/b704918f53e41f638b586ad28333eb]
Jan-24 10:31:35.728 [Actor Thread 39] INFO  nextflow.Session - [b1/096726] Submitted process > trimming (4)
Jan-24 10:31:37.671 [Actor Thread 43] INFO  nextflow.Session - [82/6d211e] Submitted process > fastqc (4)
Jan-24 10:31:37.676 [Actor Thread 39] INFO  nextflow.Session - [24/ceb424] Submitted process > mapping (4)
Jan-24 10:33:37.593 [Actor Thread 39] INFO  nextflow.Session - [77/d8aef5] Submitted process > trimming (5)
Jan-24 10:33:41.999 [Actor Thread 46] INFO  nextflow.Session - [de/7305aa] Submitted process > fastqc (5)
Jan-24 10:33:42.023 [Actor Thread 47] INFO  nextflow.Session - [9a/1ab85d] Submitted process > mapping (5)
Jan-24 10:33:46.695 [Actor Thread 39] INFO  nextflow.Session - [d6/0086a2] Submitted process > stringTie (3)
Jan-24 10:33:46.697 [Actor Thread 45] INFO  nextflow.Session - [2e/9f08d4] Submitted process > featureCounts (3)
Jan-24 10:33:46.701 [Actor Thread 49] INFO  nextflow.Session - [16/23f6d4] Submitted process > preseq (3)
Jan-24 10:36:00.102 [Thread-1] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 4 -- first: TaskHandler[id: 6; name: subsample_reads (6); status: RUNNING; exit: -; workDir: /dataB/projects/test_projects/work/a8/b704918f53e41f638b586ad28333eb]
Jan-24 10:36:00.971 [Actor Thread 54] INFO  nextflow.Session - [89/39bbe1] Submitted process > featureCounts (4)
Jan-24 10:36:00.971 [Actor Thread 50] INFO  nextflow.Session - [0f/9168ca] Submitted process > stringTie (4)
Jan-24 10:36:00.972 [Actor Thread 55] INFO  nextflow.Session - [ee/05eac9] Submitted process > preseq (4)
Jan-24 10:36:18.763 [Actor Thread 56] DEBUG nextflow.processor.TaskProcessor - <subsample_reads> Sending poison pills and terminating process
Jan-24 10:36:18.763 [Actor Thread 56] DEBUG nextflow.Session - <<< barrier arrive (process: subsample_reads)
Jan-24 10:36:18.764 [Actor Thread 62] DEBUG nextflow.processor.TaskProcessor - <trimming> Poison pill arrived
Jan-24 10:36:18.765 [Actor Thread 61] DEBUG nextflow.processor.StateObj - <trimming> State before poison: StateObj[submitted: 6; completed: 5; poisoned: false ]
Jan-24 10:36:18.770 [Actor Thread 50] INFO  nextflow.Session - [56/ba4af4] Submitted process > trimming (6)
Jan-24 10:36:18.770 [Actor Thread 62] DEBUG nextflow.processor.TaskProcessor - <trimming> After stop
Jan-24 10:36:20.538 [Actor Thread 60] DEBUG nextflow.processor.TaskProcessor - <trimming> Sending poison pills and terminating process
Jan-24 10:36:20.538 [Actor Thread 60] DEBUG nextflow.Session - <<< barrier arrive (process: trimming)
Jan-24 10:36:20.538 [Actor Thread 62] DEBUG nextflow.processor.TaskProcessor - <fastqc> Poison pill arrived
Jan-24 10:36:20.538 [Actor Thread 60] DEBUG nextflow.processor.StateObj - <fastqc> State before poison: StateObj[submitted: 6; completed: 5; poisoned: false ]
Jan-24 10:36:20.538 [Actor Thread 50] DEBUG nextflow.processor.TaskProcessor - <mapping> Poison pill arrived
Jan-24 10:36:20.539 [Actor Thread 60] DEBUG nextflow.processor.StateObj - <mapping> State before poison: StateObj[submitted: 6; completed: 4; poisoned: false ]
Jan-24 10:36:20.545 [Actor Thread 59] INFO  nextflow.Session - [d3/6590ba] Submitted process > fastqc (6)
Jan-24 10:36:20.545 [Actor Thread 62] DEBUG nextflow.processor.TaskProcessor - <fastqc> After stop
Jan-24 10:36:20.546 [Actor Thread 63] INFO  nextflow.Session - [1f/9e3614] Submitted process > mapping (6)
Jan-24 10:36:20.546 [Actor Thread 50] DEBUG nextflow.processor.TaskProcessor - <mapping> After stop
Jan-24 10:36:28.085 [Actor Thread 61] DEBUG nextflow.processor.TaskProcessor - <fastqc> Sending poison pills and terminating process
Jan-24 10:36:28.086 [Actor Thread 61] DEBUG nextflow.Session - <<< barrier arrive (process: fastqc)
Jan-24 10:37:57.870 [Actor Thread 70] INFO  nextflow.Session - [17/5d8871] Submitted process > preseq (5)
Jan-24 10:37:57.871 [Actor Thread 68] INFO  nextflow.Session - [4a/f3ad0d] Submitted process > stringTie (5)
Jan-24 10:37:57.871 [Actor Thread 66] INFO  nextflow.Session - [df/fd21b0] Submitted process > featureCounts (5)
Jan-24 10:38:54.718 [Actor Thread 60] DEBUG nextflow.processor.TaskProcessor - <qc_metrics> Sending poison pills and terminating process
Jan-24 10:38:54.718 [Actor Thread 60] DEBUG nextflow.Session - <<< barrier arrive (process: qc_metrics)
Jan-24 10:40:19.172 [Actor Thread 79] DEBUG nextflow.processor.TaskProcessor - <mapping> Sending poison pills and terminating process
Jan-24 10:40:19.173 [Actor Thread 77] DEBUG nextflow.processor.TaskProcessor - <preseq> Poison pill arrived
Jan-24 10:40:19.173 [Actor Thread 81] DEBUG nextflow.processor.TaskProcessor - <featureCounts> Poison pill arrived
Jan-24 10:40:19.173 [Actor Thread 79] DEBUG nextflow.Session - <<< barrier arrive (process: mapping)
Jan-24 10:40:19.174 [Actor Thread 82] DEBUG nextflow.processor.TaskProcessor - <stringTie> Poison pill arrived
Jan-24 10:40:19.174 [Actor Thread 75] DEBUG nextflow.processor.StateObj - <preseq> State before poison: StateObj[submitted: 6; completed: 5; poisoned: false ]
Jan-24 10:40:19.174 [Actor Thread 83] DEBUG nextflow.processor.StateObj - <featureCounts> State before poison: StateObj[submitted: 6; completed: 5; poisoned: false ]
Jan-24 10:40:19.174 [Actor Thread 79] DEBUG nextflow.processor.StateObj - <stringTie> State before poison: StateObj[submitted: 6; completed: 5; poisoned: false ]
Jan-24 10:40:19.176 [Actor Thread 78] INFO  nextflow.Session - [14/6aa6d5] Submitted process > preseq (6)
Jan-24 10:40:19.177 [Actor Thread 76] INFO  nextflow.Session - [b8/7bc446] Submitted process > stringTie (6)
Jan-24 10:40:19.177 [Actor Thread 77] DEBUG nextflow.processor.TaskProcessor - <preseq> After stop
Jan-24 10:40:19.177 [Actor Thread 82] DEBUG nextflow.processor.TaskProcessor - <stringTie> After stop
Jan-24 10:40:19.178 [Actor Thread 74] INFO  nextflow.Session - [6f/bb2ffc] Submitted process > featureCounts (6)
Jan-24 10:40:19.178 [Actor Thread 81] DEBUG nextflow.processor.TaskProcessor - <featureCounts> After stop
Jan-24 10:40:23.526 [Actor Thread 79] DEBUG nextflow.processor.TaskProcessor - <preseq> Sending poison pills and terminating process
Jan-24 10:40:23.526 [Actor Thread 79] DEBUG nextflow.Session - <<< barrier arrive (process: preseq)
Jan-24 10:40:51.897 [Actor Thread 80] DEBUG nextflow.processor.TaskProcessor - <stringTie> Sending poison pills and terminating process
Jan-24 10:40:51.897 [Actor Thread 80] DEBUG nextflow.Session - <<< barrier arrive (process: stringTie)
Jan-24 10:40:54.764 [Actor Thread 85] DEBUG nextflow.processor.TaskProcessor - <featureCounts> Sending poison pills and terminating process
Jan-24 10:40:54.765 [Actor Thread 85] DEBUG nextflow.Session - <<< barrier arrive (process: featureCounts)
Jan-24 10:40:54.765 [Actor Thread 87] DEBUG nextflow.processor.TaskProcessor - <dge> Poison pill arrived
Jan-24 10:40:54.766 [Actor Thread 89] DEBUG nextflow.processor.StateObj - <dge> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false ]
Jan-24 10:40:54.781 [Actor Thread 86] INFO  nextflow.Session - [dc/07d055] Submitted process > dge (1)
Jan-24 10:40:54.782 [Actor Thread 87] DEBUG nextflow.processor.TaskProcessor - <dge> After stop
Jan-24 10:41:25.713 [Actor Thread 85] DEBUG nextflow.processor.TaskProcessor - <dge> Sending poison pills and terminating process
Jan-24 10:41:25.713 [Thread-1] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 0 -- first: null
Jan-24 10:41:25.713 [Actor Thread 85] DEBUG nextflow.Session - <<< barrier arrive (process: dge)
Jan-24 10:41:25.900 [Actor Thread 90] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.OutOfMemoryError: Requested array size exceeds VM limit
    at java.util.Arrays.copyOf(Arrays.java:2367)
    at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
    at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:114)
    at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:415)
    at java.lang.StringBuilder.append(StringBuilder.java:132)
    at org.codehaus.groovy.runtime.InvokerHelper.formatList(InvokerHelper.java:685)
    at org.codehaus.groovy.runtime.InvokerHelper.toListString(InvokerHelper.java:785)
    at org.codehaus.groovy.runtime.InvokerHelper.toListString(InvokerHelper.java:773)
    at org.codehaus.groovy.runtime.InvokerHelper.toListString(InvokerHelper.java:762)
    at org.codehaus.groovy.runtime.InvokerHelper.write(InvokerHelper.java:508)
    at groovy.lang.GString.writeTo(GString.java:183)
    at groovy.lang.GString.toString(GString.java:155)
    at org.codehaus.groovy.reflection.stdclasses.StringCachedClass.coerceArgument(StringCachedClass.java:48)
    at org.codehaus.groovy.reflection.ParameterTypes.coerceArgumentsToClasses(ParameterTypes.java:146)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoCachedMethodSiteNoUnwrap.invoke(PojoMetaMethodSite.java:211)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at nextflow.processor.TaskProcessor$TaskProcessorInterceptor.beforeRun(TaskProcessor.groovy:2057)
    at groovyx.gpars.dataflow.operator.DataflowProcessor.fireBeforeRun(DataflowProcessor.java:371)
    at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:106)
    at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43)
    at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293)
    at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30)
    at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93)
    at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Jan-24 10:41:25.922 [Actor Thread 90] DEBUG nextflow.Session - Session aborted -- Cause: Requested array size exceeds VM limit
Jan-24 10:41:25.925 [Thread-1] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local)
Jan-24 10:41:25.926 [main] DEBUG nextflow.Session - Session await > all process finished
Jan-24 10:41:25.926 [Actor Thread 90] DEBUG nextflow.processor.TaskProcessor - <multiqc> After stop
Jan-24 10:41:25.926 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jan-24 10:41:26.031 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

[Carlos Guzman]

Easier to read the output here than on the command terminal. Requested array size exceeds VM limit. Any idea what could cause this? I've subsampled reads to 100k read each, so it can't be R. I have 132gb of RAM.

[Paolo Di Tommaso]

This looks weird. Is your code publicly accessible so that I can give it a look? 

p 

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[Carlos Guzman]

https://github.com/c-guzman/cipher-workflow-platform

In main.nf search for "PE rna".

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[Paolo Di Tommaso]

I need more debugging info. Please define the following environment variable: 

export NXF_OPTS='-XX:+HeapDumpOnOutOfMemoryError' 

Then, re-execute your pipeline. When it crashes it will create a file named `java_pidXXX.hprof`. Please share it with me (note it will be several GB, you may try to compress it). 

p

[Carlos Guzman]

Hi Paolo,

What e-mail would you like me to send the information to?

[Paolo Di Tommaso]

The mail account u can find on my Github profile.

Cheers, P