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A DSL for data-driven computational pipelines
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NullPointerException using lsf executor #1136

Closed sb10 closed 5 years ago

sb10 commented 5 years ago

Bug report

Expected behavior and actual behavior

Should submit jobs to LSF. Instead crashes after a while.

Steps to reproduce the problem

Run a workflow with lsf as the executor.

Program output

[... successful submits and completion of other tasks...]
May-02 11:13:38.794 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1353568; id: 40; name: echo_sleep (40); status: COMPLETED
; exit: 0; error: -; workDir: /lustre/scratch117/sciops/team117/npg/sb10/nextflow/wr_benchmarks/work/ce/8c6e1b22f4c5e3720c91f580e0fa95 started: 1556792018752; exited:
2019-05-02T10:13:38Z; ]
May-02 11:13:38.809 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process echo_sleep (12) > jobId: 1353577; workDir: /lustre/scratch117/sc
iops/team117/npg/sb10/nextflow/wr_benchmarks/work/8b/c85b4001712561e1d98b0378e5bf31
May-02 11:13:38.809 [Task submitter] INFO  nextflow.Session - [8b/c85b40] Submitted process > echo_sleep (12)
May-02 11:13:38.821 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'echo_sleep (42)'

Caused by:
  java.lang.NullPointerException

java.lang.NullPointerException: null
    at nextflow.util.Throttle.cache(Throttle.groovy:208)
    at nextflow.executor.AbstractGridExecutor.checkActiveStatus(AbstractGridExecutor.groovy:342)
    at nextflow.executor.AbstractGridExecutor$checkActiveStatus$0.call(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:115)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:135)
    at nextflow.executor.GridTaskHandler.readExitStatus(GridTaskHandler.groovy:205)
    at nextflow.executor.GridTaskHandler.checkIfCompleted(GridTaskHandler.groovy:326)
    at nextflow.processor.TaskPollingMonitor.checkTaskStatus(TaskPollingMonitor.groovy:601)
    at nextflow.processor.TaskPollingMonitor.checkAllTasks(TaskPollingMonitor.groovy:528)
    at nextflow.processor.TaskPollingMonitor.pollLoop(TaskPollingMonitor.groovy:407)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:101)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1217)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041)
    at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1011)
    at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:994)
    at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:97)
    at nextflow.processor.TaskPollingMonitor$_start_closure2.doCall(TaskPollingMonitor.groovy:291)
    at nextflow.processor.TaskPollingMonitor$_start_closure2.call(TaskPollingMonitor.groovy)
    at groovy.lang.Closure.run(Closure.java:486)
    at java.lang.Thread.run(Thread.java:748)
May-02 11:13:38.841 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: java.lang.NullPointerException

Environment

Additional context

This is with my own build of my own fork, and the build was done on a Mac and the result of make pack copied to a linux machine. For some reason I have to do java -jar nextflow, because just ./nextflow fails with another reason. So this could just be related to a build oddity.

But I know you changed polling-related things recently, so perhaps this is a real bug.

pditommaso commented 5 years ago

Could you please include the .nextflow.log file?

sb10 commented 5 years ago

Don't know how to attach a file. But the error message above came from .nextflow.log. Everything else in the file was just normal operation.

pditommaso commented 5 years ago

It contains more details that would allow me to troubleshoot the issue. You should be able to attach to this issue or share using pastebin.com

pditommaso commented 5 years ago

I'm closing this because I'm unable to replicate the issue.

olgabot commented 5 years ago

@sb10 were you able to solve this? I'm seeing the same issue with Nextflow version 19.07.0-edge

.nextflow.log

``` Aug-03 16:39:14.537 [main] DEBUG nextflow.cli.Launcher - $> nextflow run /data_sm/home/olga_ibm/code/nf-core/find-splice-motifs/main.nf --a_splice_junctions '/data_sm/home/olga_ibm/data_sm/czb-maca/Plate_seq/sj_out_tab/3_month/170907_A00111_0051_BH2HWLDMXX/results_gencode_ercc/A10-D*SJ.out.tab' --b_bed 'eclip/*.bed' --additional_options \'-u\' --outdir /data_sm/home/olga_ibm/data_lg/czb-maca/Plate_seq/nf-kmer-intersect-results/ --protein_name HNRNPL --kmers hnrnpl_rna_bind-n-seq_kmers_zscore_greaterthan_2_noheader.csv --conservation_bed 'conservation/*.bed' --fasta /home/olga/data_lg/czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.fa --custom_config_base /data_sm/home/olga_ibm/code/nf-core/configs/ -profile czbiohub_lsf -w /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/ -resume Aug-03 16:39:14.909 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 19.07.0-edge Aug-03 16:39:14.963 [main] INFO nextflow.cli.CmdRun - Launching `/data_sm/home/olga_ibm/code/nf-core/find-splice-motifs/main.nf` [suspicious_dijkstra] - revision: b8a80a6785 Aug-03 16:39:14.984 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /data_sm/home/olga_ibm/code/nf-core/find-splice-motifs/nextflow.config Aug-03 16:39:14.985 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data_sm/home/olga_ibm/code/nf-core/find-splice-motifs/nextflow.config Aug-03 16:39:15.038 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `czbiohub_lsf` Aug-03 16:39:16.840 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [uppmax_devel, bigpurple, uppmax, docker, gis, ccga, conda, singularity, munin, prince, czbiohub_aws, hebbe, cfc, uzh, debug, test_kmers, test, czbiohub_lsf, crick, czbiohub_aws_highpriority, phoenix, shh, mendel, uct_hex, awsbatch, binac] Aug-03 16:39:16.916 [main] DEBUG nextflow.Session - Session uuid: e6248fd2-5857-45da-8997-33d49d15acdd Aug-03 16:39:16.916 [main] DEBUG nextflow.Session - Run name: suspicious_dijkstra Aug-03 16:39:16.917 [main] DEBUG nextflow.Session - Executor pool size: 64 Aug-03 16:39:16.934 [main] DEBUG nextflow.cli.CmdRun - Version: 19.07.0-edge build 5103 Created: 09-07-2019 11:46 UTC (04:46 PDT) System: Linux 4.14.0-115.el7a.ppc64le Runtime: Groovy 2.5.6 on OpenJDK 64-Bit Server VM 1.8.0_212-b04 Encoding: UTF-8 (UTF-8) Process: 14807@fury.czbiohub.org [192.168.99.80] CPUs: 64 - Mem: 123.8 GB (41 GB) - Swap: 4 GB (4 GB) Aug-03 16:39:17.036 [main] DEBUG nextflow.Session - Work-dir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm [gpfs] Aug-03 16:39:17.822 [main] DEBUG nextflow.Session - Session start invoked Aug-03 16:39:17.827 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /data_sm/home/olga_ibm/data_lg/czb-maca/Plate_seq/nf-kmer-intersect-results/pipeline_info/nf-core/bedtools-intersect_trace.txt Aug-03 16:39:18.932 [main] WARN nextflow.Session - There's no process matching config selector: fastqc Aug-03 16:39:18.932 [main] WARN nextflow.Session - There's no process matching config selector: multiqc Aug-03 16:39:18.933 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Aug-03 16:39:19.184 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: conservation/; pattern: *.bed; options: [:] Aug-03 16:39:19.206 [PathVisitor-2] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data_sm/home/olga_ibm/data_sm/czb-maca/Plate_seq/sj_out_tab/3_month/170907_A00111_0051_BH2HWLDMXX/results_gencode_ercc/; pattern: A10-D*SJ.out.tab; options: [:] Aug-03 16:39:19.209 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: eclip/; pattern: *.bed; options: [:] Aug-03 16:39:19.215 [main] WARN nextflow.extension.IntoOp - The `into` operator should be used to connect two or more target channels -- consider to replace it with `.set { input_bed_b }` Aug-03 16:39:19.218 [main] INFO nextflow.Nextflow - ======================================================= ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/bedtools-intersect v1.0dev" ======================================================= Aug-03 16:39:19.230 [main] INFO nextflow.Nextflow - Pipeline Name : nf-core/bedtools-intersect Pipeline Version: 1.0dev Run Name : suspicious_dijkstra (A) Splice junctions: /data_sm/home/olga_ibm/data_sm/czb-maca/Plate_seq/sj_out_tab/3_month/170907_A00111_0051_BH2HWLDMXX/results_gencode_ercc/A10-D*SJ.out.tab (B) Bed files : eclip/*.bed k-mers : hnrnpl_rna_bind-n-seq_kmers_zscore_greaterthan_2_noheader.csv No. mismatches in k-mer: 0 Protein name : HNRNPL Save prefs : Individual Motifs: No / Genome-wide Motif bed: No Max Memory : 1.9 TB Max CPUs : 96 Max Time : 10d Output dir : /data_sm/home/olga_ibm/data_lg/czb-maca/Plate_seq/nf-kmer-intersect-results/ Working dir : /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm Container Engine: docker Container : czbiohub/splicemotifs:latest Current home : /data_sm/home/olga_ibm Current user : olga Current path : /data_sm/home/olga_ibm/code/maca-data-analysis/analysis-scripts/hnrnpl Script dir : /data_sm/home/olga_ibm/code/nf-core/find-splice-motifs Config Profile : czbiohub_lsf Aug-03 16:39:19.232 [main] INFO nextflow.Nextflow - ========================================= Aug-03 16:39:19.297 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-03 16:39:19.297 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-03 16:39:19.311 [main] DEBUG nextflow.executor.Executor - [warm up] executor > lsf Aug-03 16:39:19.317 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'lsf' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Aug-03 16:39:19.333 [main] DEBUG nextflow.executor.LsfExecutor - [LSF] Detected lsf.conf LSF_UNIT_FOR_LIMITS=MB Aug-03 16:39:19.393 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > get_software_versions -- maxForks: 64 Aug-03 16:39:19.448 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-03 16:39:19.449 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-03 16:39:19.451 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > seq2profile -- maxForks: 64 Aug-03 16:39:19.520 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-03 16:39:19.521 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-03 16:39:19.547 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [0] Aug-03 16:39:19.571 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > scanMotifGenomeWide -- maxForks: 64 Aug-03 16:39:19.617 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-03 16:39:19.617 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-03 16:39:19.619 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [1] Aug-03 16:39:19.623 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > motif_intersect_with_conservation -- maxForks: 64 Aug-03 16:39:19.899 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-03 16:39:19.899 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-03 16:39:19.902 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > concatenate_conserved_motifs -- maxForks: 64 Aug-03 16:39:19.924 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-03 16:39:19.925 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-03 16:39:19.926 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > sj2bed -- maxForks: 64 Aug-03 16:39:19.950 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-03 16:39:19.951 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-03 16:39:19.953 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [0] Aug-03 16:39:19.955 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > junction_line_count -- maxForks: 64 Aug-03 16:39:19.970 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-03 16:39:19.970 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-03 16:39:20.010 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [0, 1] Aug-03 16:39:20.013 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bedtools_intersect -- maxForks: 64 Aug-03 16:39:20.043 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-03 16:39:20.044 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-03 16:39:20.048 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > intersection_line_count -- maxForks: 64 Aug-03 16:39:20.078 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-03 16:39:20.079 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-03 16:39:20.081 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > combine_intersection_and_line_count -- maxForks: 64 Aug-03 16:39:20.106 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-03 16:39:20.107 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-03 16:39:20.111 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > merge_counts -- maxForks: 64 Aug-03 16:39:20.129 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-03 16:39:20.130 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-03 16:39:20.132 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > transpose_counts -- maxForks: 64 Aug-03 16:39:20.140 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Aug-03 16:39:20.140 [main] DEBUG nextflow.Session - Session await Aug-03 16:39:20.267 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACCAC) > jobId: 1533; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/2c/1b41a54cb7261159b6394c1b35d6e2 Aug-03 16:39:20.273 [Task submitter] INFO nextflow.Session - [2c/1b41a5] Submitted process > seq2profile (ACCAC) Aug-03 16:39:20.422 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CATGC) > jobId: 1534; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/b8/84c68750900a41f4d18c5644d3e0c8 Aug-03 16:39:20.423 [Task submitter] INFO nextflow.Session - [b8/84c687] Submitted process > seq2profile (CATGC) Aug-03 16:39:20.570 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATAAA) > jobId: 1535; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/0b/1a306956a964cece32785cf87ab5e0 Aug-03 16:39:20.571 [Task submitter] INFO nextflow.Session - [0b/1a3069] Submitted process > seq2profile (ATAAA) Aug-03 16:39:20.701 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATAAC) > jobId: 1536; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/86/1029ec6b5a9cc5621e7f8fbe99c8eb Aug-03 16:39:20.703 [Task submitter] INFO nextflow.Session - [86/1029ec] Submitted process > seq2profile (ATAAC) Aug-03 16:39:20.844 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATCAC) > jobId: 1537; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/c6/f7bcc4610902af9bdaa0d2fa687ec6 Aug-03 16:39:20.844 [Task submitter] INFO nextflow.Session - [c6/f7bcc4] Submitted process > seq2profile (ATCAC) Aug-03 16:39:20.925 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TACAA) > jobId: 1538; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/44/abaa12182d16698bf91b4d631cbe47 Aug-03 16:39:20.926 [Task submitter] INFO nextflow.Session - [44/abaa12] Submitted process > seq2profile (TACAA) Aug-03 16:39:21.012 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACACA) > jobId: 1539; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/92/59872366c533d24c07b97b509b8c16 Aug-03 16:39:21.012 [Task submitter] INFO nextflow.Session - [92/598723] Submitted process > seq2profile (ACACA) Aug-03 16:39:21.092 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CCCAC) > jobId: 1540; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/02/d0e537ebc2cb00738b98308b24aa51 Aug-03 16:39:21.092 [Task submitter] INFO nextflow.Session - [02/d0e537] Submitted process > seq2profile (CCCAC) Aug-03 16:39:21.166 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACACC) > jobId: 1541; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/6d/7ee6c94ef3c0e8d9d69a7831d17c0e Aug-03 16:39:21.167 [Task submitter] INFO nextflow.Session - [6d/7ee6c9] Submitted process > seq2profile (ACACC) Aug-03 16:39:21.240 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACGCA) > jobId: 1542; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/08/e165e56c5b76ddc686e96741dcf1a9 Aug-03 16:39:21.240 [Task submitter] INFO nextflow.Session - [08/e165e5] Submitted process > seq2profile (ACGCA) Aug-03 16:39:21.318 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (AATAC) > jobId: 1543; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/8a/f176e1fc7858aa5a92f504b88eec71 Aug-03 16:39:21.318 [Task submitter] INFO nextflow.Session - [8a/f176e1] Submitted process > seq2profile (AATAC) Aug-03 16:39:21.390 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CACAG) > jobId: 1544; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/f4/efc151e68f9533fa675ff5afe62ad3 Aug-03 16:39:21.391 [Task submitter] INFO nextflow.Session - [f4/efc151] Submitted process > seq2profile (CACAG) Aug-03 16:39:21.436 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CACTA) > jobId: 1545; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/16/6cb95ab7fc1d76258e66c0a442d05f Aug-03 16:39:21.436 [Task submitter] INFO nextflow.Session - [16/6cb95a] Submitted process > seq2profile (CACTA) Aug-03 16:39:21.483 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACATC) > jobId: 1546; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/c9/9d2c79004e4bb52c727b30d429a8d5 Aug-03 16:39:21.484 [Task submitter] INFO nextflow.Session - [c9/9d2c79] Submitted process > seq2profile (ACATC) Aug-03 16:39:21.528 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CGCAC) > jobId: 1547; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/aa/666ddb7daeb5f3e2fa477d5a6f26da Aug-03 16:39:21.529 [Task submitter] INFO nextflow.Session - [aa/666ddb] Submitted process > seq2profile (CGCAC) Aug-03 16:39:21.579 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TCACA) > jobId: 1548; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/70/7dfea84e64e50ee82724471c1b8f13 Aug-03 16:39:21.580 [Task submitter] INFO nextflow.Session - [70/7dfea8] Submitted process > seq2profile (TCACA) Aug-03 16:39:21.629 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATATT) > jobId: 1549; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/4b/08c8e413d5b551b75901952b77189a Aug-03 16:39:21.629 [Task submitter] INFO nextflow.Session - [4b/08c8e4] Submitted process > seq2profile (ATATT) Aug-03 16:39:21.666 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATTCA) > jobId: 1550; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/06/a46ad927178ce1787bb47451f65b08 Aug-03 16:39:21.666 [Task submitter] INFO nextflow.Session - [06/a46ad9] Submitted process > seq2profile (ATTCA) Aug-03 16:39:21.705 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (AACAT) > jobId: 1551; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/d0/31dc1fb1cf8ce0174ac6576ff17855 Aug-03 16:39:21.705 [Task submitter] INFO nextflow.Session - [d0/31dc1f] Submitted process > seq2profile (AACAT) Aug-03 16:39:21.743 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATTAC) > jobId: 1552; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/58/841a45ab6d73aef773d7afeaa1e158 Aug-03 16:39:21.743 [Task submitter] INFO nextflow.Session - [58/841a45] Submitted process > seq2profile (ATTAC) Aug-03 16:39:21.777 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CAACA) > jobId: 1553; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/4a/decbed622ec81870f09fadf9b10687 Aug-03 16:39:21.777 [Task submitter] INFO nextflow.Session - [4a/decbed] Submitted process > seq2profile (CAACA) Aug-03 16:39:21.808 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (GCATA) > jobId: 1554; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/50/6c97b14cf76c6d9f0b2abd2cd71c17 Aug-03 16:39:21.808 [Task submitter] INFO nextflow.Session - [50/6c97b1] Submitted process > seq2profile (GCATA) Aug-03 16:39:21.840 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACAAC) > jobId: 1555; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/77/1b71ef2347bc84b6aeab9ff36468da Aug-03 16:39:21.840 [Task submitter] INFO nextflow.Session - [77/1b71ef] Submitted process > seq2profile (ACAAC) Aug-03 16:39:21.872 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (AGCAC) > jobId: 1556; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/0a/dbc9be77775c8a357d005298ea6427 Aug-03 16:39:21.872 [Task submitter] INFO nextflow.Session - [0a/dbc9be] Submitted process > seq2profile (AGCAC) Aug-03 16:39:21.903 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CTACA) > jobId: 1557; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/9f/19a0a28064295beec6f9cfe4791526 Aug-03 16:39:21.904 [Task submitter] INFO nextflow.Session - [9f/19a0a2] Submitted process > seq2profile (CTACA) Aug-03 16:39:21.949 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TATAC) > jobId: 1558; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/34/2f3ec64229dfdbfa6b68bbe18ac066 Aug-03 16:39:21.949 [Task submitter] INFO nextflow.Session - [34/2f3ec6] Submitted process > seq2profile (TATAC) Aug-03 16:39:21.978 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TGCAC) > jobId: 1559; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/16/cbfaea0f7f331f90bba996a7f70966 Aug-03 16:39:21.978 [Task submitter] INFO nextflow.Session - [16/cbfaea] Submitted process > seq2profile (TGCAC) Aug-03 16:39:22.003 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TCATA) > jobId: 1560; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/16/6c4982b971f3cee2e5d6b95b183a57 Aug-03 16:39:22.003 [Task submitter] INFO nextflow.Session - [16/6c4982] Submitted process > seq2profile (TCATA) Aug-03 16:39:22.029 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CATTA) > jobId: 1561; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/32/a991b1e7dade30960be165ba0c204f Aug-03 16:39:22.030 [Task submitter] INFO nextflow.Session - [32/a991b1] Submitted process > seq2profile (CATTA) Aug-03 16:39:22.054 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CAAAC) > jobId: 1562; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/bc/e01dc85449cfe82e2871121eb6562c Aug-03 16:39:22.054 [Task submitter] INFO nextflow.Session - [bc/e01dc8] Submitted process > seq2profile (CAAAC) Aug-03 16:39:22.078 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TTCAC) > jobId: 1563; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/cc/cf015020467802646abdd69451ffde Aug-03 16:39:22.078 [Task submitter] INFO nextflow.Session - [cc/cf0150] Submitted process > seq2profile (TTCAC) Aug-03 16:39:22.105 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CACAT) > jobId: 1564; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/07/b58ad6c38661c0fc83dbf600e08f09 Aug-03 16:39:22.105 [Task submitter] INFO nextflow.Session - [07/b58ad6] Submitted process > seq2profile (CACAT) Aug-03 16:39:22.128 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CACAC) > jobId: 1565; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/39/19e05e2f17f00b8be6ffc9bcb3f218 Aug-03 16:39:22.128 [Task submitter] INFO nextflow.Session - [39/19e05e] Submitted process > seq2profile (CACAC) Aug-03 16:39:22.152 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (AACAC) > jobId: 1566; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/59/4f59fbb13fc8dbbcfd4ecb7d9cb857 Aug-03 16:39:22.152 [Task submitter] INFO nextflow.Session - [59/4f59fb] Submitted process > seq2profile (AACAC) Aug-03 16:39:22.172 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATGCA) > jobId: 1567; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/71/6bdb457ce072a5e0d97c6f9fae63ec Aug-03 16:39:22.173 [Task submitter] INFO nextflow.Session - [71/6bdb45] Submitted process > seq2profile (ATGCA) Aug-03 16:39:22.192 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACACT) > jobId: 1568; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/26/f700bf97d90f84fdd8c9b928679a3b Aug-03 16:39:22.193 [Task submitter] INFO nextflow.Session - [26/f700bf] Submitted process > seq2profile (ACACT) Aug-03 16:39:22.213 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CACAA) > jobId: 1569; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/e5/e2388ce09c3397e79d04f25abbc1e5 Aug-03 16:39:22.213 [Task submitter] INFO nextflow.Session - [e5/e2388c] Submitted process > seq2profile (CACAA) Aug-03 16:39:22.232 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (AAACA) > jobId: 1570; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/87/528af87876aeffc935c6c23bef5bed Aug-03 16:39:22.233 [Task submitter] INFO nextflow.Session - [87/528af8] Submitted process > seq2profile (AAACA) Aug-03 16:39:22.253 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CACCA) > jobId: 1571; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/23/b0b3158487aa4b34f7a1f01619dd6f Aug-03 16:39:22.254 [Task submitter] INFO nextflow.Session - [23/b0b315] Submitted process > seq2profile (CACCA) Aug-03 16:39:22.273 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACAAA) > jobId: 1572; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/4f/7d66d33b02f08559099503a75b60a6 Aug-03 16:39:22.273 [Task submitter] INFO nextflow.Session - [4f/7d66d3] Submitted process > seq2profile (ACAAA) Aug-03 16:39:22.298 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process get_software_versions > jobId: 1573; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/4d/949450c74cfcf599accab5093be613 Aug-03 16:39:22.298 [Task submitter] INFO nextflow.Session - [4d/949450] Submitted process > get_software_versions Aug-03 16:39:22.339 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CCACA) > jobId: 1574; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/21/e56c137c5013ba9d2d3b54b76b455f Aug-03 16:39:22.340 [Task submitter] INFO nextflow.Session - [21/e56c13] Submitted process > seq2profile (CCACA) Aug-03 16:39:22.363 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CATAA) > jobId: 1575; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/55/ea6693729b74a01b56534b590b99f2 Aug-03 16:39:22.363 [Task submitter] INFO nextflow.Session - [55/ea6693] Submitted process > seq2profile (CATAA) Aug-03 16:39:22.383 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TATAT) > jobId: 1576; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/ee/60407baa3094dbbf0fced84e976808 Aug-03 16:39:22.383 [Task submitter] INFO nextflow.Session - [ee/60407b] Submitted process > seq2profile (TATAT) Aug-03 16:39:22.412 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CAATA) > jobId: 1577; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/c4/56fb7f085eeba690898c415552e409 Aug-03 16:39:22.412 [Task submitter] INFO nextflow.Session - [c4/56fb7f] Submitted process > seq2profile (CAATA) Aug-03 16:39:22.433 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACATG) > jobId: 1578; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/2b/996d46646dd2b8d0d4287941e419ff Aug-03 16:39:22.433 [Task submitter] INFO nextflow.Session - [2b/996d46] Submitted process > seq2profile (ACATG) Aug-03 16:39:22.454 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CATTC) > jobId: 1579; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/fa/a4176b18a2a9296387280320a32c3c Aug-03 16:39:22.454 [Task submitter] INFO nextflow.Session - [fa/a4176b] Submitted process > seq2profile (CATTC) Aug-03 16:39:22.475 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACATA) > jobId: 1580; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/08/22dca77033230bf7cdb4c9366f0f31 Aug-03 16:39:22.475 [Task submitter] INFO nextflow.Session - [08/22dca7] Submitted process > seq2profile (ACATA) Aug-03 16:39:22.496 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATATA) > jobId: 1581; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/e7/e7056a2fceb2517cd9a36b9ef6666f Aug-03 16:39:22.497 [Task submitter] INFO nextflow.Session - [e7/e7056a] Submitted process > seq2profile (ATATA) Aug-03 16:39:22.517 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CATCA) > jobId: 1582; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/55/05bc2c7e92b9554e2489e8a7eb0041 Aug-03 16:39:22.517 [Task submitter] INFO nextflow.Session - [55/05bc2c] Submitted process > seq2profile (CATCA) Aug-03 16:39:22.535 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACATT) > jobId: 1583; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/71/cd37aafcba1f8773e9747ab46254e4 Aug-03 16:39:22.536 [Task submitter] INFO nextflow.Session - [71/cd37aa] Submitted process > seq2profile (ACATT) Aug-03 16:39:22.556 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TAACA) > jobId: 1584; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/d1/210b29dfe59477666fc7ee473be72d Aug-03 16:39:22.556 [Task submitter] INFO nextflow.Session - [d1/210b29] Submitted process > seq2profile (TAACA) Aug-03 16:39:22.574 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACACG) > jobId: 1585; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/86/97c8d17c5cdddea1de03bd1aa1a9cd Aug-03 16:39:22.575 [Task submitter] INFO nextflow.Session - [86/97c8d1] Submitted process > seq2profile (ACACG) Aug-03 16:39:22.594 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CACGC) > jobId: 1586; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/20/584d3d0a63bded571cd5cd7311b8d8 Aug-03 16:39:22.594 [Task submitter] INFO nextflow.Session - [20/584d3d] Submitted process > seq2profile (CACGC) Aug-03 16:39:22.627 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TACAT) > jobId: 1587; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/bf/5f8b4eadefe8d71ef8c0f006d76a80 Aug-03 16:39:22.627 [Task submitter] INFO nextflow.Session - [bf/5f8b4e] Submitted process > seq2profile (TACAT) Aug-03 16:39:22.651 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATACA) > jobId: 1588; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/34/640b471fe8d47970724d5f11127074 Aug-03 16:39:22.651 [Task submitter] INFO nextflow.Session - [34/640b47] Submitted process > seq2profile (ATACA) Aug-03 16:39:22.669 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACAAT) > jobId: 1589; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/f5/1c414655b97f12eb5a19cee8590882 Aug-03 16:39:22.670 [Task submitter] INFO nextflow.Session - [f5/1c4146] Submitted process > seq2profile (ACAAT) Aug-03 16:39:22.689 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACTAC) > jobId: 1590; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/56/2aa7d83f079904d62a40e48df1cecb Aug-03 16:39:22.689 [Task submitter] INFO nextflow.Session - [56/2aa7d8] Submitted process > seq2profile (ACTAC) Aug-03 16:39:22.708 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (GCACA) > jobId: 1591; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/1b/c59e396c96bd6820db78c423461bb1 Aug-03 16:39:22.708 [Task submitter] INFO nextflow.Session - [1b/c59e39] Submitted process > seq2profile (GCACA) Aug-03 16:39:22.727 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TACAC) > jobId: 1592; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/b9/18f963ba90fb6f05fdada611792136 Aug-03 16:39:22.727 [Task submitter] INFO nextflow.Session - [b9/18f963] Submitted process > seq2profile (TACAC) Aug-03 16:39:22.750 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CATAT) > jobId: 1593; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/a8/43bfe873e954c508daf5af14332600 Aug-03 16:39:22.750 [Task submitter] INFO nextflow.Session - [a8/43bfe8] Submitted process > seq2profile (CATAT) Aug-03 16:39:22.769 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CATAC) > jobId: 1594; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/6b/1a3b6ebfa08e84b710c8f6ec6444af Aug-03 16:39:22.769 [Task submitter] INFO nextflow.Session - [6b/1a3b6e] Submitted process > seq2profile (CATAC) Aug-03 16:39:22.788 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CATTT) > jobId: 1595; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/85/36eead84a9c40fbc9d82b8cb14bff7 Aug-03 16:39:22.789 [Task submitter] INFO nextflow.Session - [85/36eead] Submitted process > seq2profile (CATTT) Aug-03 16:39:22.807 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (AAATA) > jobId: 1596; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/a5/a049a4e635ba0fb05651002eab7c50 Aug-03 16:39:22.807 [Task submitter] INFO nextflow.Session - [a5/a049a4] Submitted process > seq2profile (AAATA) Aug-03 16:39:22.826 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TTACA) > jobId: 1597; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/29/165265633c3703a888bca0ec61ef2e Aug-03 16:39:22.826 [Task submitter] INFO nextflow.Session - [29/165265] Submitted process > seq2profile (TTACA) Aug-03 16:39:22.845 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CACTT) > jobId: 1598; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/0c/06933ddac98d6fcd530f03f1ece20e Aug-03 16:39:22.845 [Task submitter] INFO nextflow.Session - [0c/06933d] Submitted process > seq2profile (CACTT) Aug-03 16:39:22.867 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CTCAC) > jobId: 1599; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/36/f39b97b6875ab3daa63820cc20ce0e Aug-03 16:39:22.868 [Task submitter] INFO nextflow.Session - [36/f39b97] Submitted process > seq2profile (CTCAC) Aug-03 16:39:22.887 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACAGC) > jobId: 1600; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/31/c98c8248481ae993e528f87af20dde Aug-03 16:39:22.887 [Task submitter] INFO nextflow.Session - [31/c98c82] Submitted process > seq2profile (ACAGC) Aug-03 16:39:22.905 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CAGCA) > jobId: 1601; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/29/97c5df250528a1c5fb604ad990b15d Aug-03 16:39:22.906 [Task submitter] INFO nextflow.Session - [29/97c5df] Submitted process > seq2profile (CAGCA) Aug-03 16:39:22.927 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CCATA) > jobId: 1602; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/1d/571b621164c69ef15c59d88cf32b6b Aug-03 16:39:22.927 [Task submitter] INFO nextflow.Session - [1d/571b62] Submitted process > seq2profile (CCATA) Aug-03 16:39:22.958 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CCCCA) > jobId: 1603; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/73/6b4e4f0b6f02eb7560f0ca5ab967c0 Aug-03 16:39:22.958 [Task submitter] INFO nextflow.Session - [73/6b4e4f] Submitted process > seq2profile (CCCCA) Aug-03 16:39:22.995 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATACT) > jobId: 1604; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/b0/1c63c84c778fe49a1b499093675363 Aug-03 16:39:22.996 [Task submitter] INFO nextflow.Session - [b0/1c63c8] Submitted process > seq2profile (ATACT) Aug-03 16:39:23.039 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (AACAA) > jobId: 1605; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/4e/95d690b22f62c7fdba8ffe5348e8d6 Aug-03 16:39:23.040 [Task submitter] INFO nextflow.Session - [4e/95d690] Submitted process > seq2profile (AACAA) Aug-03 16:39:23.062 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (AATAT) > jobId: 1606; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/d7/ef8a5fdf5914600ce3c92fd0a18acd Aug-03 16:39:23.063 [Task submitter] INFO nextflow.Session - [d7/ef8a5f] Submitted process > seq2profile (AATAT) Aug-03 16:39:23.083 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CACCC) > jobId: 1607; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/b5/dc29e23b4e7ad0b0523eebfe6ccfb4 Aug-03 16:39:23.083 [Task submitter] INFO nextflow.Session - [b5/dc29e2] Submitted process > seq2profile (CACCC) Aug-03 16:39:23.109 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACTCA) > jobId: 1608; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/75/3a9129e9ae4bfe8b4cd1ea27c61be5 Aug-03 16:39:23.110 [Task submitter] INFO nextflow.Session - [75/3a9129] Submitted process > seq2profile (ACTCA) Aug-03 16:39:23.129 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATACC) > jobId: 1609; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/bf/623c153746a1dbb2759a6b587508b5 Aug-03 16:39:23.129 [Task submitter] INFO nextflow.Session - [bf/623c15] Submitted process > seq2profile (ATACC) Aug-03 16:39:23.148 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CATCC) > jobId: 1610; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/b8/1e8990d07a7f561905eec0f06d1800 Aug-03 16:39:23.148 [Task submitter] INFO nextflow.Session - [b8/1e8990] Submitted process > seq2profile (CATCC) Aug-03 16:39:23.169 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATTTA) > jobId: 1611; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/56/b7bb746ec134caafa8fdc77c4adba4 Aug-03 16:39:23.169 [Task submitter] INFO nextflow.Session - [56/b7bb74] Submitted process > seq2profile (ATTTA) Aug-03 16:39:23.187 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CCTCA) > jobId: 1612; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/29/78f3a6d0ce53dd7a834fb701c6f94b Aug-03 16:39:23.188 [Task submitter] INFO nextflow.Session - [29/78f3a6] Submitted process > seq2profile (CCTCA) Aug-03 16:39:23.206 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATAAT) > jobId: 1613; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/5f/cf37401371b88a626cf205fe691d81 Aug-03 16:39:23.206 [Task submitter] INFO nextflow.Session - [5f/cf3740] Submitted process > seq2profile (ATAAT) Aug-03 16:39:23.224 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TTATA) > jobId: 1614; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/e3/75b8f677b70835e7fe75d178be3152 Aug-03 16:39:23.225 [Task submitter] INFO nextflow.Session - [e3/75b8f6] Submitted process > seq2profile (TTATA) Aug-03 16:39:23.243 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACCCA) > jobId: 1615; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/cf/1fa4a39f04dbd8548b9e138dac7dff Aug-03 16:39:23.243 [Task submitter] INFO nextflow.Session - [cf/1fa4a3] Submitted process > seq2profile (ACCCA) Aug-03 16:39:23.261 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATATC) > jobId: 1616; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/61/391708b50cf440d32f3e54475fe72a Aug-03 16:39:23.261 [Task submitter] INFO nextflow.Session - [61/391708] Submitted process > seq2profile (ATATC) Aug-03 16:39:23.281 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ACCAT) > jobId: 1617; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/7d/c7057908e285c26dda20e39cb81a3a Aug-03 16:39:23.281 [Task submitter] INFO nextflow.Session - [7d/c70579] Submitted process > seq2profile (ACCAT) Aug-03 16:39:23.302 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CGCAT) > jobId: 1618; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/83/bb4a559f74b22586beea417ce0806e Aug-03 16:39:23.303 [Task submitter] INFO nextflow.Session - [83/bb4a55] Submitted process > seq2profile (CGCAT) Aug-03 16:39:23.321 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (AACCC) > jobId: 1619; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/90/4f4e7e9ef498c50ff4afb7931d5969 Aug-03 16:39:23.321 [Task submitter] INFO nextflow.Session - [90/4f4e7e] Submitted process > seq2profile (AACCC) Aug-03 16:39:23.340 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (ATCAT) > jobId: 1620; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/dc/4abce252794e292e606bf4da466056 Aug-03 16:39:23.341 [Task submitter] INFO nextflow.Session - [dc/4abce2] Submitted process > seq2profile (ATCAT) Aug-03 16:39:23.359 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CAAAT) > jobId: 1621; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/dc/70878191114352208c9a442e241f7a Aug-03 16:39:23.359 [Task submitter] INFO nextflow.Session - [dc/708781] Submitted process > seq2profile (CAAAT) Aug-03 16:39:23.377 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CACTC) > jobId: 1622; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/b8/773d321470ab1ff90303268b191ec9 Aug-03 16:39:23.377 [Task submitter] INFO nextflow.Session - [b8/773d32] Submitted process > seq2profile (CACTC) Aug-03 16:39:23.395 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TAAAC) > jobId: 1623; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/5b/faa66dd8dd232546ff6551e6f16d40 Aug-03 16:39:23.395 [Task submitter] INFO nextflow.Session - [5b/faa66d] Submitted process > seq2profile (TAAAC) Aug-03 16:39:23.414 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CCAAC) > jobId: 1624; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/1a/d9424302d33703db4a90cd2e2132f1 Aug-03 16:39:23.414 [Task submitter] INFO nextflow.Session - [1a/d94243] Submitted process > seq2profile (CCAAC) Aug-03 16:39:23.432 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (GTACA) > jobId: 1625; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/ef/a974fa2c51837841ef4e5835b5ba06 Aug-03 16:39:23.432 [Task submitter] INFO nextflow.Session - [ef/a974fa] Submitted process > seq2profile (GTACA) Aug-03 16:39:23.450 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (GCACC) > jobId: 1626; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/88/9926ba35c67407dbadcd9a3014745d Aug-03 16:39:23.450 [Task submitter] INFO nextflow.Session - [88/9926ba] Submitted process > seq2profile (GCACC) Aug-03 16:39:23.470 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CAAAA) > jobId: 1627; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/f8/f3cbbd1c5da8da05962e4a9f6ef3f3 Aug-03 16:39:23.470 [Task submitter] INFO nextflow.Session - [f8/f3cbbd] Submitted process > seq2profile (CAAAA) Aug-03 16:39:23.488 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TTTAC) > jobId: 1628; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/12/377b3bff6d17ebc8ccb8bf5454539b Aug-03 16:39:23.489 [Task submitter] INFO nextflow.Session - [12/377b3b] Submitted process > seq2profile (TTTAC) Aug-03 16:39:23.507 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (AACCA) > jobId: 1629; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/92/67d11872847e3c746a2a6a075f7815 Aug-03 16:39:23.507 [Task submitter] INFO nextflow.Session - [92/67d118] Submitted process > seq2profile (AACCA) Aug-03 16:39:23.525 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (TATCA) > jobId: 1630; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/47/726b0d61996740f80bcd079d27505b Aug-03 16:39:23.525 [Task submitter] INFO nextflow.Session - [47/726b0d] Submitted process > seq2profile (TATCA) Aug-03 16:39:23.543 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CCGCA) > jobId: 1631; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/66/6cb537fe0af4cb890852e4a0630b91 Aug-03 16:39:23.543 [Task submitter] INFO nextflow.Session - [66/6cb537] Submitted process > seq2profile (CCGCA) Aug-03 16:39:23.561 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process seq2profile (CCCAT) > jobId: 1632; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates-ibm/19/3aedd685af768e0f97e1092a6dc7f3 Aug-03 16:39:23.561 [Task submitter] INFO nextflow.Session - [19/3aedd6] Submitted process > seq2profile (CCCAT) Aug-03 16:39:24.346 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'seq2profile (ACCAC)' Caused by: java.lang.NullPointerException java.lang.NullPointerException: null at nextflow.util.Throttle.cache(Throttle.groovy:208) at nextflow.executor.AbstractGridExecutor.getQueueStatus(AbstractGridExecutor.groovy:299) at nextflow.executor.AbstractGridExecutor.checkStartedStatus(AbstractGridExecutor.groovy:345) at nextflow.executor.AbstractGridExecutor$checkStartedStatus$5.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:115) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:135) at nextflow.executor.GridTaskHandler.isStarted(GridTaskHandler.groovy:309) at nextflow.executor.GridTaskHandler.checkIfRunning(GridTaskHandler.groovy:290) at nextflow.processor.TaskPollingMonitor.checkTaskStatus(TaskPollingMonitor.groovy:596) at nextflow.processor.TaskPollingMonitor.checkAllTasks(TaskPollingMonitor.groovy:528) at nextflow.processor.TaskPollingMonitor.pollLoop(TaskPollingMonitor.groovy:407) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:101) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1217) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041) at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1011) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:994) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:97) at nextflow.processor.TaskPollingMonitor$_start_closure2.doCall(TaskPollingMonitor.groovy:291) at nextflow.processor.TaskPollingMonitor$_start_closure2.call(TaskPollingMonitor.groovy) at groovy.lang.Closure.run(Closure.java:486) at java.lang.Thread.run(Thread.java:748) Aug-03 16:39:24.359 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: java.lang.NullPointerException Aug-03 16:39:24.388 [Task monitor] DEBUG nextflow.Session - The following nodes are still active: [process] scanMotifGenomeWide status=ACTIVE port 0: (value) OPEN ; channel: __$eachinparam<0> port 1: (queue) OPEN ; channel: genome_fasta port 2: (cntrl) - ; channel: $ [process] motif_intersect_with_conservation status=ACTIVE port 0: (queue) OPEN ; channel: conservation port 1: (value) OPEN ; channel: __$eachinparam<1> port 2: (cntrl) - ; channel: $ [process] concatenate_conserved_motifs status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] junction_line_count status=ACTIVE port 0: (value) OPEN ; channel: __$eachinparam<0> port 1: (cntrl) - ; channel: $ [process] bedtools_intersect status=ACTIVE port 0: (value) OPEN ; channel: __$eachinparam<0> port 1: (value) OPEN ; channel: __$eachinparam<1> port 2: (cntrl) - ; channel: $ [process] intersection_line_count status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] combine_intersection_and_line_count status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] merge_counts status=ACTIVE port 0: (value) OPEN ; channel: input_files port 1: (value) OPEN ; channel: sample_names port 2: (cntrl) - ; channel: $ [process] transpose_counts status=ACTIVE port 0: (value) OPEN ; channel: counts port 1: (cntrl) - ; channel: $ Aug-03 16:39:24.392 [main] DEBUG nextflow.Session - Session await > all process finished Aug-03 16:39:24.392 [main] DEBUG nextflow.Session - Session await > all barriers passed Aug-03 16:39:24.502 [main] INFO nextflow.Nextflow - [nf-core/bedtools-intersect] Pipeline Complete Aug-03 16:39:24.506 [main] WARN n.processor.TaskPollingMonitor - Killing pending tasks (100) Aug-03 16:39:25.440 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=0; failedCount=100; ignoredCount=0; cachedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms] Aug-03 16:39:25.441 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file Aug-03 16:39:25.447 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report Aug-03 16:39:25.585 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: {"seq2profile":{"cpu":null,"mem":null,"vmem":null,"time":null,"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"get_software_versions":{"cpu":null,"mem":null,"vmem":null,"time":null,"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null}} Aug-03 16:39:27.449 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline Aug-03 16:39:27.500 [main] WARN nextflow.dag.GraphvizRenderer - To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info. Aug-03 16:39:27.596 [main] DEBUG nextflow.CacheDB - Closing CacheDB done Aug-03 16:39:27.625 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye ```
olgabot commented 5 years ago

This happens with a standard pipeline like nf-core/rnaseq as well:

``` Aug-06 10:56:42.839 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -profile test,czbiohub_lsf . --custom_config_base /data_sm/home/olga_ibm/code/nf-core/configs/ Aug-06 10:56:43.162 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 19.07.0-edge Aug-06 10:56:44.658 [main] INFO nextflow.cli.CmdRun - Launching `./main.nf` [maniac_bartik] - revision: 292e705d20 Aug-06 10:56:44.673 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data_sm/home/olga_ibm/code/nf-core/rnaseq/nextflow.config Aug-06 10:56:44.673 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data_sm/home/olga_ibm/code/nf-core/rnaseq/nextflow.config Aug-06 10:56:44.687 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,czbiohub_lsf` Aug-06 10:56:45.663 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [uppmax_devel, bigpurple, uppmax, docker, gis, ccga, conda, singularity, munin, prince, czbiohub_aws, hebbe, cfc, uzh, debug, test, czbiohub_lsf, crick, czbiohub_aws_highpriority, phoenix, shh, mendel, uct_hex, awsbatch, binac] Aug-06 10:56:45.722 [main] DEBUG nextflow.Session - Session uuid: ef1f962b-d9d7-49ae-afa7-faacc73d005d Aug-06 10:56:45.722 [main] DEBUG nextflow.Session - Run name: maniac_bartik Aug-06 10:56:45.723 [main] DEBUG nextflow.Session - Executor pool size: 64 Aug-06 10:56:45.737 [main] DEBUG nextflow.cli.CmdRun - Version: 19.07.0-edge build 5103 Created: 09-07-2019 11:46 UTC (04:46 PDT) System: Linux 4.14.0-115.el7a.ppc64le Runtime: Groovy 2.5.6 on OpenJDK 64-Bit Server VM 1.8.0_212-b04 Encoding: UTF-8 (UTF-8) Process: 1471@fury.czbiohub.org [192.168.99.80] CPUs: 64 - Mem: 123.8 GB (39.1 GB) - Swap: 4 GB (4 GB) Aug-06 10:56:45.961 [main] DEBUG nextflow.Session - Work-dir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates [gpfs] Aug-06 10:56:46.559 [main] DEBUG nextflow.Session - Session start invoked Aug-06 10:56:46.564 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /data_sm/home/olga_ibm/code/nf-core/rnaseq/results/pipeline_info/execution_trace.txt Aug-06 10:56:48.495 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Aug-06 10:56:48.717 [main] INFO nextflow.Nextflow - ---------------------------------------------------- ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/rnaseq v1.4dev ---------------------------------------------------- Aug-06 10:56:48.725 [main] INFO nextflow.Nextflow - Run Name : maniac_bartik Reads : data/*{1,2}.fastq.gz Data Type : Single-End Strandedness : None Trimming : 5'R1: 0 / 5'R2: 0 / 3'R1: 0 / 3'R2: 0 / NextSeq Trim: 0 Aligner : STAR Fasta Ref : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa GTF Annotation : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf Biotype GTF field : gene_type Save prefs : Ref Genome: Yes / Trimmed FastQ: No / Alignment intermediates: No Max Resources : 6 GB memory, 2 cpus, 2d time per job Container : docker - nfcore/rnaseq:dev Output dir : ./results Launch dir : /data_sm/home/olga_ibm/code/nf-core/rnaseq Working dir : /data_sm/home/olga_ibm/data_lg/nextflow-intermediates Script dir : /data_sm/home/olga_ibm/code/nf-core/rnaseq User : olga Config Profile : test,czbiohub_lsf Config Description: Minimal test dataset to check pipeline function Config Contact : Olga Botvinnik (@olgabot) Config URL : https://www.czbiohub.org/ Aug-06 10:56:48.726 [main] INFO nextflow.Nextflow - ---------------------------------------------------- Aug-06 10:56:48.794 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:get_software_versions` matches process get_software_versions Aug-06 10:56:48.799 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:48.799 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:48.813 [main] DEBUG nextflow.executor.Executor - [warm up] executor > lsf Aug-06 10:56:48.818 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'lsf' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Aug-06 10:56:48.833 [main] DEBUG nextflow.executor.LsfExecutor - [LSF] Detected lsf.conf LSF_UNIT_FOR_LIMITS=MB Aug-06 10:56:48.883 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > get_software_versions -- maxForks: 64 Aug-06 10:56:48.933 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:48.933 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:48.935 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeBED12 -- maxForks: 64 Aug-06 10:56:48.943 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:high_memory` matches label `high_memory` for process with name makeSTARindex Aug-06 10:56:48.945 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:48.945 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:48.947 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeSTARindex -- maxForks: 64 Aug-06 10:56:48.970 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:48.970 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:48.971 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 64 Aug-06 10:56:49.018 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:low_memory` matches label `low_memory` for process with name trim_galore Aug-06 10:56:49.018 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:trim_galore` matches process trim_galore Aug-06 10:56:49.022 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:49.022 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:49.024 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > trim_galore -- maxForks: 64 Aug-06 10:56:49.107 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:high_memory` matches label `high_memory` for process with name star Aug-06 10:56:49.110 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:49.110 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:49.112 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > star -- maxForks: 64 Aug-06 10:56:49.182 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mid_memory` matches label `mid_memory` for process with name rseqc Aug-06 10:56:49.186 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:49.186 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:49.188 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > rseqc -- maxForks: 64 Aug-06 10:56:49.206 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:49.206 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:49.209 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > preseq -- maxForks: 64 Aug-06 10:56:49.227 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:markDuplicates` matches process markDuplicates Aug-06 10:56:49.232 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:49.232 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:49.233 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > markDuplicates -- maxForks: 64 Aug-06 10:56:49.248 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:low_memory` matches label `low_memory` for process with name qualimap Aug-06 10:56:49.251 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:49.251 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:49.253 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > qualimap -- maxForks: 64 Aug-06 10:56:49.270 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:low_memory` matches label `low_memory` for process with name dupradar Aug-06 10:56:49.273 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:49.273 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:49.275 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > dupradar -- maxForks: 64 Aug-06 10:56:49.295 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:low_memory` matches label `low_memory` for process with name featureCounts Aug-06 10:56:49.299 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:49.299 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:49.300 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > featureCounts -- maxForks: 64 Aug-06 10:56:49.327 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mid_memory` matches label `mid_memory` for process with name merge_featureCounts Aug-06 10:56:49.337 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:49.337 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:49.341 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > merge_featureCounts -- maxForks: 64 Aug-06 10:56:49.363 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:49.363 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:49.365 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > stringtieFPKM -- maxForks: 64 Aug-06 10:56:49.402 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:low_memory` matches label `low_memory` for process with name sample_correlation Aug-06 10:56:49.407 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:49.407 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:49.409 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > sample_correlation -- maxForks: 64 Aug-06 10:56:49.426 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process get_software_versions > jobId: 1640; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/f7/5c49dddee6278412fe43d35759e1eb Aug-06 10:56:49.430 [Task submitter] INFO nextflow.Session - [f7/5c49dd] Submitted process > get_software_versions Aug-06 10:56:49.524 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:multiqc` matches process multiqc Aug-06 10:56:49.526 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:49.526 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:49.530 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > multiqc -- maxForks: 64 Aug-06 10:56:49.564 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: lsf Aug-06 10:56:49.564 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'lsf' Aug-06 10:56:49.565 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > output_documentation -- maxForks: 64 Aug-06 10:56:49.568 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Aug-06 10:56:49.568 [main] DEBUG nextflow.Session - Session await Aug-06 10:56:49.720 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process output_documentation (1) > jobId: 1641; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/e7/93842b85c621f3faaccbecbbcdc672 Aug-06 10:56:49.720 [Task submitter] INFO nextflow.Session - [e7/93842b] Submitted process > output_documentation (1) Aug-06 10:56:50.021 [Actor Thread 5] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=192; maxQueueSize=576; keepAlive=1m Aug-06 10:56:50.029 [FileTransfer-thread-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/SRR4238351_subsamp.fastq.gz at /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/stage/ef/d86174c4bc20c4142afecd16c51cee/SRR4238351_subsamp.fastq.gz Aug-06 10:56:50.505 [FileTransfer-thread-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/SRR4238355_subsamp.fastq.gz at /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/stage/da/7f02dc7e5fafef457e82009f57264a/SRR4238355_subsamp.fastq.gz Aug-06 10:56:50.621 [FileTransfer-thread-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/SRR4238379_subsamp.fastq.gz at /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/stage/5b/d09a43f5e85391de6b96aed4cef517/SRR4238379_subsamp.fastq.gz Aug-06 10:56:50.694 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process fastqc (SRR4238355) > jobId: 1642; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/c9/2c8284103500fcbd5d762b03d47e1e Aug-06 10:56:50.694 [Task submitter] INFO nextflow.Session - [c9/2c8284] Submitted process > fastqc (SRR4238355) Aug-06 10:56:50.726 [FileTransfer-thread-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf at /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/stage/d3/52a7fab01c82b8bc38eb59a77be87a/genes.gtf Aug-06 10:56:50.747 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process trim_galore (SRR4238355) > jobId: 1643; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/8f/38dbf5fbc7cd8be110b587b38f53f6 Aug-06 10:56:50.747 [Task submitter] INFO nextflow.Session - [8f/38dbf5] Submitted process > trim_galore (SRR4238355) Aug-06 10:56:50.814 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process trim_galore (SRR4238351) > jobId: 1644; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/0c/96ca4d99c834ae049b93875a8421df Aug-06 10:56:50.815 [Task submitter] INFO nextflow.Session - [0c/96ca4d] Submitted process > trim_galore (SRR4238351) Aug-06 10:56:50.850 [FileTransfer-thread-5] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/testdata/SRR4238359_subsamp.fastq.gz at /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/stage/29/5ef8dc851382f1d084040dc663d0c6/SRR4238359_subsamp.fastq.gz Aug-06 10:56:50.912 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process trim_galore (SRR4238379) > jobId: 1645; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/de/7b928da904ebb94d0237260f48e6a8 Aug-06 10:56:50.912 [Task submitter] INFO nextflow.Session - [de/7b928d] Submitted process > trim_galore (SRR4238379) Aug-06 10:56:50.946 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process fastqc (SRR4238359) > jobId: 1646; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/95/e42372ce75d987c9790a3931a04d53 Aug-06 10:56:50.947 [Task submitter] INFO nextflow.Session - [95/e42372] Submitted process > fastqc (SRR4238359) Aug-06 10:56:50.978 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process fastqc (SRR4238379) > jobId: 1647; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/22/f88f71e989bc0ec637980e095821ac Aug-06 10:56:50.978 [Task submitter] INFO nextflow.Session - [22/f88f71] Submitted process > fastqc (SRR4238379) Aug-06 10:56:51.014 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process trim_galore (SRR4238359) > jobId: 1648; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/bb/faa697910675e7d78e7c3444806dbd Aug-06 10:56:51.014 [Task submitter] INFO nextflow.Session - [bb/faa697] Submitted process > trim_galore (SRR4238359) Aug-06 10:56:51.048 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process fastqc (SRR4238351) > jobId: 1649; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/a4/33ad5abf14e72c9fb0cbdccddbf2d7 Aug-06 10:56:51.048 [Task submitter] INFO nextflow.Session - [a4/33ad5a] Submitted process > fastqc (SRR4238351) Aug-06 10:56:51.077 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process makeBED12 (genes.gtf) > jobId: 1650; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/e4/07174f2f395a1828ee8167b096c645 Aug-06 10:56:51.078 [Task submitter] INFO nextflow.Session - [e4/07174f] Submitted process > makeBED12 (genes.gtf) Aug-06 10:56:51.120 [FileTransfer-thread-6] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa at /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/stage/54/d07064b63861fcc404fc09e9212284/genome.fa Aug-06 10:56:51.231 [FileTransfer-thread-7] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf at /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/stage/d3/52a7fab01c82b8bc38eb59a77be87a/genes.gtf Aug-06 10:56:51.294 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [LSF] submitted process makeSTARindex (genome.fa) > jobId: 1651; workDir: /data_sm/home/olga_ibm/data_lg/nextflow-intermediates/ad/87fc8d8215034b1a1ca04cc2032be9 Aug-06 10:56:51.294 [Task submitter] INFO nextflow.Session - [ad/87fc8d] Submitted process > makeSTARindex (genome.fa) Aug-06 10:56:53.838 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'get_software_versions' Caused by: java.lang.NullPointerException java.lang.NullPointerException: null at nextflow.util.Throttle.cache(Throttle.groovy:208) at nextflow.executor.AbstractGridExecutor.getQueueStatus(AbstractGridExecutor.groovy:299) at nextflow.executor.AbstractGridExecutor.checkStartedStatus(AbstractGridExecutor.groovy:345) at nextflow.executor.AbstractGridExecutor$checkStartedStatus$0.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:115) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:135) at nextflow.executor.GridTaskHandler.isStarted(GridTaskHandler.groovy:309) at nextflow.executor.GridTaskHandler.checkIfRunning(GridTaskHandler.groovy:290) at nextflow.processor.TaskPollingMonitor.checkTaskStatus(TaskPollingMonitor.groovy:596) at nextflow.processor.TaskPollingMonitor.checkAllTasks(TaskPollingMonitor.groovy:528) at nextflow.processor.TaskPollingMonitor.pollLoop(TaskPollingMonitor.groovy:407) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:101) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1217) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041) at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1011) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:994) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:97) at nextflow.processor.TaskPollingMonitor$_start_closure2.doCall(TaskPollingMonitor.groovy:291) at nextflow.processor.TaskPollingMonitor$_start_closure2.call(TaskPollingMonitor.groovy) at groovy.lang.Closure.run(Closure.java:486) at java.lang.Thread.run(Thread.java:748) Aug-06 10:56:53.849 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: java.lang.NullPointerException Aug-06 10:56:53.894 [Task monitor] DEBUG nextflow.Session - The following nodes are still active: [process] star status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) OPEN ; channel: index port 2: (value) bound ; channel: gtf port 3: (value) bound ; channel: wherearemyfiles port 4: (cntrl) - ; channel: $ [process] rseqc status=ACTIVE port 0: (queue) OPEN ; channel: bam_rseqc port 1: (queue) OPEN ; channel: index port 2: (value) OPEN ; channel: bed12 port 3: (cntrl) - ; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN ; channel: bam_preseq port 1: (cntrl) - ; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN ; channel: bam port 1: (cntrl) - ; channel: $ [process] qualimap status=ACTIVE port 0: (queue) OPEN ; channel: bam port 1: (value) bound ; channel: gtf port 2: (cntrl) - ; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN ; channel: bam_md port 1: (value) bound ; channel: gtf port 2: (cntrl) - ; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN ; channel: bam_featurecounts port 1: (value) bound ; channel: gtf port 2: (value) bound ; channel: biotypes_header port 3: (cntrl) - ; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) OPEN ; channel: input_files port 1: (cntrl) - ; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN ; channel: bam_stringtieFPKM port 1: (value) bound ; channel: gtf port 2: (cntrl) - ; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) OPEN ; channel: input_files port 1: (value) OPEN ; channel: num_bams port 2: (queue) OPEN ; channel: mdsplot_header port 3: (queue) OPEN ; channel: heatmap_header port 4: (cntrl) - ; channel: $ [process] multiqc status=ACTIVE port 0: (value) bound ; channel: multiqc_config port 1: (value) OPEN ; channel: fastqc port 2: (value) OPEN ; channel: trimgalore/* port 3: (value) OPEN ; channel: alignment/* port 4: (value) OPEN ; channel: rseqc/* port 5: (value) OPEN ; channel: qualimap/* port 6: (value) OPEN ; channel: preseq/* port 7: (value) OPEN ; channel: dupradar/* port 8: (value) OPEN ; channel: featureCounts/* port 9: (value) OPEN ; channel: featureCounts_biotype/* port 10: (value) bound ; channel: salmon/* port 11: (value) OPEN ; channel: sample_correlation_results/* port 12: (value) OPEN ; channel: software_versions/* port 13: (value) bound ; channel: workflow_summary port 14: (cntrl) - ; channel: $ Aug-06 10:56:53.897 [main] DEBUG nextflow.Session - Session await > all process finished Aug-06 10:56:53.898 [main] DEBUG nextflow.Session - Session await > all barriers passed Aug-06 10:56:54.148 [main] INFO nextflow.Nextflow - [nf-core/rnaseq] Pipeline completed with errors Aug-06 10:56:54.152 [main] WARN n.processor.TaskPollingMonitor - Killing pending tasks (12) Aug-06 10:56:54.280 [main] DEBUG n.executor.AbstractGridExecutor - Unable to kill pending jobs - cmd executed: bkill 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 - exit status : 255 - output : Job <1640>: Job has already finished Job <1641>: Job has already finished Job <1642>: Job has already finished Job <1643>: Job has already finished Job <1645>: Job has already finished Job <1644> is being terminated Job <1646> is being terminated Job <1647> is being terminated Job <1648> is being terminated Job <1649> is being terminated Job <1650> is being terminated Job <1651> is being terminated Aug-06 10:56:54.281 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=0; failedCount=12; ignoredCount=0; cachedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms] Aug-06 10:56:54.281 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file Aug-06 10:56:54.285 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report Aug-06 10:56:54.366 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: {"makeSTARindex":{"cpu":null,"mem":null,"vmem":null,"time":null,"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"get_software_versions":{"cpu":null,"mem":null,"vmem":null,"time":null,"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"output_documentation":{"cpu":null,"mem":null,"vmem":null,"time":null,"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"fastqc":{"cpu":null,"mem":null,"vmem":null,"time":null,"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"trim_galore":{"cpu":null,"mem":null,"vmem":null,"time":null,"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"makeBED12":{"cpu":null,"mem":null,"vmem":null,"time":null,"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null}} Aug-06 10:56:56.450 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline Aug-06 10:56:56.527 [main] WARN nextflow.dag.GraphvizRenderer - To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info. Aug-06 10:56:56.625 [main] DEBUG nextflow.CacheDB - Closing CacheDB done Aug-06 10:56:56.643 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye ```

EDIT: use nf-core/rnaseq output

pditommaso commented 5 years ago

This was fixed by #1234. Update to the latest version.

olgabot commented 5 years ago

Thank you, it seems to be working now!

Olga Botvinnik, PhD olgabotvinnik.com http://www.olgabotvinnik.com

On Tue, Aug 6, 2019 at 12:27 PM Paolo Di Tommaso notifications@github.com wrote:

This was fixed by #1234 https://github.com/nextflow-io/nextflow/issues/1234. Update to the latest version.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/nextflow-io/nextflow/issues/1136?email_source=notifications&email_token=AAGE24B2I2VEQCYXLXJEI33QDHGBBA5CNFSM4HJ5CFOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3WGQ2A#issuecomment-518809704, or mute the thread https://github.com/notifications/unsubscribe-auth/AAGE24CJBZDNI7XLNOY4HELQDHGBBANCNFSM4HJ5CFOA .