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the chipseq pipeline runs forever even when errors were reported #298

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gudeqing opened this issue Aug 26, 2022 · 2 comments
Closed

the chipseq pipeline runs forever even when errors were reported #298

gudeqing opened this issue Aug 26, 2022 · 2 comments

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@gudeqing
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Hi, I found the chipseq pipeline will run forever even when error reported!

The command used to launch the workflow was as follows:

 nextflow run nf-core/chipseq --input design.csv --fasta /testdata/genome.fa --gtf /testdata/genes.gtf -qs 5 --macs_gsize 2.7e9 -offline --outdir /enigma/local_storage/ -resume

Pipeline Configuration:

  • Run Name: cheeky_cray
  • Data Type: Paired-End
  • Design File: design.csv
  • Genome: Not supplied
  • Fasta File: /testdata/genome.fa
  • GTF File: /testdata/genes.gtf
  • MACS2 Genome Size: 2.7e9
  • Min Consensus Reps: 1
  • MACS2 Narrow Peaks: No
  • MACS2 Broad Cutoff: 0.1
  • Trim R1: 0 bp
  • Trim R2: 0 bp
  • Trim 3' R1: 0 bp
  • Trim 3' R2: 0 bp
  • NextSeq Trim: 0 bp
  • Fingerprint Bins: 500000
  • Save Genome Index: No
  • Max Resources: 128 GB memory, 16 cpus, 10d time per job
  • Output Dir: /enigma/local_storage/
  • Launch Dir: /enigma/local_storage
  • Working Dir: /enigma/local_storage/work
  • Script Dir: /root/.nextflow/assets/nf-core/chipseq
  • User: root
  • Config Profile: standard
  • Date Started: 2022-08-26T07:40:32.843487Z
  • Date Completed: 2022-08-26T08:17:04.528705Z
  • Pipeline script file path: /root/.nextflow/assets/nf-core/chipseq/main.nf
  • Pipeline script hash ID: 39c073c68caf34f6f725e82907fff2bd
  • Pipeline repository Git URL: https://github.com/nf-core/chipseq
  • Pipeline repository Git Commit: 6924b66
  • Pipeline Git branch/tag: master
  • Nextflow Version: 21.10.6
  • Nextflow Build: 5660
  • Nextflow Compile Timestamp: 21-12-2021 16:55 UTC

running status:
image

tail of the ,nexflow.log：
Aug-26 07:40:35.833 [main] DEBUG nextflow.Session - Session await > all barriers passed
Aug-26 07:40:35.833 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/mqc_spp_nsc_plot.png
Aug-26 07:40:35.833 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/mqc_picard_insert_size_plot.png
Aug-26 07:40:35.833 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/mqc_deseq2_sample_similarity_plot.png
Aug-26 07:40:35.833 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/nf-core-chipseq_logo.png
Aug-26 07:40:35.834 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/mqc_macs2_peak_count_plot.png
Aug-26 07:40:35.834 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/mqc_samtools_stats_plot.png
Aug-26 07:40:35.834 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/mqc_picard_deduplication_plot.png
Aug-26 07:40:35.834 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/mqc_deseq2_pca_plot.png
Aug-26 07:40:35.835 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/r_deseq2_ma_plot.png
Aug-26 07:40:35.835 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/mqc_cutadapt_plot.png
Aug-26 07:40:35.835 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/r_upsetr_intersect_plot.png
Aug-26 07:40:35.835 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/igv_screenshot.png
Aug-26 07:40:35.836 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/mqc_preseq_plot.png
Aug-26 07:40:35.836 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/mqc_deeptools_plotProfile_plot.png
Aug-26 07:40:35.836 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/mqc_spp_rsc_plot.png
Aug-26 07:40:35.849 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/mqc_deeptools_plotFingerprint_plot.png
Aug-26 07:40:35.850 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/docs/images/r_deseq2_volcano_plot.png
Aug-26 07:40:35.851 [Actor Thread 4] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/nf-core/chipseq/bin/markdown_to_html.py
Aug-26 07:40:35.920 [Actor Thread 13] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.012 s; total time: 0.013 s
Aug-26 07:40:35.931 [Actor Thread 13] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/eaf0fedf6e6e51441522aa82438c6ceb.collect-file
Aug-26 07:40:35.938 [Actor Thread 13] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-5332452955947821456
Aug-26 07:45:35.811 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 5 -- tasks to be submitted are shown below
~> TaskHandler[id: 1; name: CHECK_DESIGN (design.csv); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/f7/5558e2114cac76f90c9bcf645f0c3d]
~> TaskHandler[id: 3; name: MAKE_GENE_BED (genes.gtf); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/17/47fa87ef9ca0eb84430ba45fa044a0]
~> TaskHandler[id: 4; name: MAKE_GENOME_FILTER (genome.fa); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/e0/ed57245c94a8c32a708c64395e9fc1]
~> TaskHandler[id: 5; name: get_software_versions; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/70/408ad1bfd0414bb74be618bfc9d71c]
~> TaskHandler[id: 6; name: output_documentation; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/b8/e098c250e24fd2563f6b587bf1e4e9]
Aug-26 07:50:35.955 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 5 -- tasks to be submitted are shown below
~> TaskHandler[id: 1; name: CHECK_DESIGN (design.csv); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/f7/5558e2114cac76f90c9bcf645f0c3d]
~> TaskHandler[id: 3; name: MAKE_GENE_BED (genes.gtf); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/17/47fa87ef9ca0eb84430ba45fa044a0]
~> TaskHandler[id: 4; name: MAKE_GENOME_FILTER (genome.fa); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/e0/ed57245c94a8c32a708c64395e9fc1]
~> TaskHandler[id: 5; name: get_software_versions; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/70/408ad1bfd0414bb74be618bfc9d71c]
~> TaskHandler[id: 6; name: output_documentation; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/b8/e098c250e24fd2563f6b587bf1e4e9]
Aug-26 07:55:36.087 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 5 -- tasks to be submitted are shown below
~> TaskHandler[id: 1; name: CHECK_DESIGN (design.csv); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/f7/5558e2114cac76f90c9bcf645f0c3d]
~> TaskHandler[id: 3; name: MAKE_GENE_BED (genes.gtf); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/17/47fa87ef9ca0eb84430ba45fa044a0]
~> TaskHandler[id: 4; name: MAKE_GENOME_FILTER (genome.fa); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/e0/ed57245c94a8c32a708c64395e9fc1]
~> TaskHandler[id: 5; name: get_software_versions; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/70/408ad1bfd0414bb74be618bfc9d71c]
~> TaskHandler[id: 6; name: output_documentation; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/b8/e098c250e24fd2563f6b587bf1e4e9]
Aug-26 08:00:36.221 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 5 -- tasks to be submitted are shown below
~> TaskHandler[id: 1; name: CHECK_DESIGN (design.csv); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/f7/5558e2114cac76f90c9bcf645f0c3d]
~> TaskHandler[id: 3; name: MAKE_GENE_BED (genes.gtf); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/17/47fa87ef9ca0eb84430ba45fa044a0]
~> TaskHandler[id: 4; name: MAKE_GENOME_FILTER (genome.fa); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/e0/ed57245c94a8c32a708c64395e9fc1]
~> TaskHandler[id: 5; name: get_software_versions; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/70/408ad1bfd0414bb74be618bfc9d71c]
~> TaskHandler[id: 6; name: output_documentation; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/b8/e098c250e24fd2563f6b587bf1e4e9]
Aug-26 08:05:36.352 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 5 -- tasks to be submitted are shown below
~> TaskHandler[id: 1; name: CHECK_DESIGN (design.csv); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/f7/5558e2114cac76f90c9bcf645f0c3d]
~> TaskHandler[id: 3; name: MAKE_GENE_BED (genes.gtf); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/17/47fa87ef9ca0eb84430ba45fa044a0]
~> TaskHandler[id: 4; name: MAKE_GENOME_FILTER (genome.fa); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/e0/ed57245c94a8c32a708c64395e9fc1]
~> TaskHandler[id: 5; name: get_software_versions; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/70/408ad1bfd0414bb74be618bfc9d71c]
~> TaskHandler[id: 6; name: output_documentation; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/b8/e098c250e24fd2563f6b587bf1e4e9]
Aug-26 08:10:36.484 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 5 -- tasks to be submitted are shown below
~> TaskHandler[id: 1; name: CHECK_DESIGN (design.csv); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/f7/5558e2114cac76f90c9bcf645f0c3d]
~> TaskHandler[id: 3; name: MAKE_GENE_BED (genes.gtf); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/17/47fa87ef9ca0eb84430ba45fa044a0]
~> TaskHandler[id: 4; name: MAKE_GENOME_FILTER (genome.fa); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/e0/ed57245c94a8c32a708c64395e9fc1]
~> TaskHandler[id: 5; name: get_software_versions; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/70/408ad1bfd0414bb74be618bfc9d71c]
~> TaskHandler[id: 6; name: output_documentation; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/b8/e098c250e24fd2563f6b587bf1e4e9]
Aug-26 08:15:36.612 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 5 -- tasks to be submitted are shown below
~> TaskHandler[id: 1; name: CHECK_DESIGN (design.csv); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/f7/5558e2114cac76f90c9bcf645f0c3d]
~> TaskHandler[id: 3; name: MAKE_GENE_BED (genes.gtf); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/17/47fa87ef9ca0eb84430ba45fa044a0]
~> TaskHandler[id: 4; name: MAKE_GENOME_FILTER (genome.fa); status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/e0/ed57245c94a8c32a708c64395e9fc1]
~> TaskHandler[id: 5; name: get_software_versions; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/70/408ad1bfd0414bb74be618bfc9d71c]
~> TaskHandler[id: 6; name: output_documentation; status: NEW; exit: -; error: -; workDir: /enigma/local_storage/work/b8/e098c250e24fd2563f6b587bf1e4e9]
@JoseEspinosa
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Hi @gudeqing, thanks for reporting
Could it be that there are still running jobs, Nextflow tries to safely finish all the jobs before stopping. Otherwise, I can not figure out the reason, maybe @drpatelh has another better guess 🤔

@JoseEspinosa
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Will close it now since it did not have activity, feel free to reach out if you have any further question

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@JoseEspinosa @gudeqing