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funnel 0.10 truncates output on text view of a task #642

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kmavrommatis opened this issue Jul 22, 2020 · 0 comments
Open

funnel 0.10 truncates output on text view of a task #642

kmavrommatis opened this issue Jul 22, 2020 · 0 comments

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@kmavrommatis
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Hi,
when I use the latest docker image for funnel (0.10) I get the following line in system logs, where the cmd line is truncated

level info
msg Running command
timestamp 2020-07-21T20:33:18.056019729Z
task_attempt 0
executor_index 0
cmd docker run -i --read-only --rm -e HOME

while the JSON tab has the full command.
similarly when I view the same task on the previous version (0.9) the cmd appears complete:

level info
msg Running command
timestamp 2020-07-21T20:33:18.056019729Z
task_attempt 0
executor_index 0
cmd docker run -i --read-only --rm -e HOME=/tmp/502d0ab2-b816-4c8f-a8ee-aff29be11b0d/root/atac_seq_bamqc/phantompeakqualtools_chip -e TMPDIR=/tmp/502d0ab2-b816-4c8f-a8ee-aff29be11b0d/root/atac_seq_bamqc/phantompeakqualtools_chip --name bsbl1m12rmo000e6t470-0 -w /tmp/502d0ab2-b816-4c8f-a8ee-aff29be11b0d/root/atac_seq_bamqc/phantompeakqualtools_chip -v /opt/funnel-work-dir/bsbl1m12rmo000e6t470/tmp:/tmp:rw -v /opt/funnel-work-dir/bsbl1m12rmo000e6t470/rnd/funnel/502d0ab2-b816-4c8f-a8ee-aff29be11b0d/root/atac_seq_bamqc/picard_markduplicates_1/32-KG1-ATAC-Dup2.mdup.bai:/rnd/funnel/502d0ab2-b816-4c8f-a8ee-aff29be11b0d/root/atac_seq_bamqc/picard_markduplicates_1/32-KG1-ATAC-Dup2.mdup.bai:ro -v /opt/funnel-work-dir/bsbl1m12rmo000e6t470/rnd/funnel/502d0ab2-b816-4c8f-a8ee-aff29be11b0d/root/atac_seq_bamqc/picard_markduplicates_1/32-KG1-ATAC-Dup2.mdup.bam:/rnd/funnel/502d0ab2-b816-4c8f-a8ee-aff29be11b0d/root/atac_seq_bamqc/picard_markduplicates_1/32-KG1-ATAC-Dup2.mdup.bam:ro 064965165932.dkr.ecr.us-east-1.amazonaws.com/ngs/phantompeakqualtools:v1.2 /bin/sh -c Rscript --verbose --max-ppsize=500000 /usr/bin/phantompeakqualtools-1.2/run_spp.R -tmpdir=/tmp/502d0ab2-b816-4c8f-a8ee-aff29be11b0d/root/atac_seq_bamqc/phantompeakqualtools_chip -odir=/tmp/502d0ab2-b816-4c8f-a8ee-aff29be11b0d/root/atac_seq_bamqc/phantompeakqualtools_chip -c=/celgene-rnd-riku-researchanalytics/funnel/502d0ab2-b816-4c8f-a8ee-aff29be11b0d/root/atac_seq_bamqc/picard_markduplicates_1/32-KG1-ATAC-Dup2.mdup.bam -savp=null-32-KG1-ATAC-Dup2.crosscor.pdf -out=null-32-KG1-ATAC-Dup2.spp.out

Thanks in advance for your help

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