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Error with 1_scATAC_mito.sh #5

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ysq1770368148 opened this issue Feb 12, 2022 · 0 comments
Open

Error with 1_scATAC_mito.sh #5

ysq1770368148 opened this issue Feb 12, 2022 · 0 comments

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@ysq1770368148
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Hi,when I use 1_scATAC_mito.sh script, I have the following problems, can you help me with these problems?

Adapter trimming: in-house script (02-12 19:45:47) elapsed: 0.0 TIME

Found lock file: /share/home/linlab/yangsuqin/ATAC-mito/test/example/outputtest/sc_output/13-TAAGGCGA-GCGATCTA/lock.raw__13-TAAGGCGA-GCGATCTA_R1.trim.fastq
Overwriting target...
Target to produce: /share/home/linlab/yangsuqin/ATAC-mito/test/example/outputtest/sc_output/13-TAAGGCGA-GCGATCTA/raw/13-TAAGGCGA-GCGATCTA_R1.trim.fastq
/bin/sh: /home/jinxu/pipeline_pypiper/ATAC_mito_sc/src/adapterTrimming: No such file or directory

/home/jinxu/pipeline_pypiper/ATAC_mito_sc/src/adapterTrimming /share/home/linlab/yangsuqin/ATAC-mito/test/example/outputtest/sc_output/13-TAAGGCGA-GCGATCTA/raw/13-TAAGGCGA-GCGATCTA_R1.fastq.gz /share/home/linlab/yangsuqin/ATAC-mito/test/example/outputtest/sc_output/13-TAAGGCGA-GCGATCTA/raw/13-TAAGGCGA-GCGATCTA_R2.fastq.gz (246493)


Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 246493; Command: /home/jinxu/pipeline_pypiper/ATAC_mito_sc/src/adapterTrimming; Return code: 127; Memory used: 0.0GB

Pipeline failed at: (02-12 19:45:47) elapsed: 0.0 TIME

Total time: 0:00:04
Failure reason: Subprocess returned nonzero result. Check above output for details
Traceback (most recent call last):
File "/share/home/linlab/yangsuqin/ATAC-mito/ATAC_mito_sc/src/scATACseq_mtSMC_3.py", line 107, in
pm.run(cmd,trimmed_fastq)
File "/share/home/linlab/yangsuqin/.local/lib/python3.9/site-packages/pypiper/manager.py", line 785, in run
self.callprint(cmd, shell, lock_file, nofail, container) # Run command
File "/share/home/linlab/yangsuqin/.local/lib/python3.9/site-packages/pypiper/manager.py", line 1028, in callprint
self._triage_error(SubprocessError(msg), nofail)
File "/share/home/linlab/yangsuqin/.local/lib/python3.9/site-packages/pypiper/manager.py", line 2131, in _triage_error
self.fail_pipeline(e)
File "/share/home/linlab/yangsuqin/.local/lib/python3.9/site-packages/pypiper/manager.py", line 1660, in fail_pipeline
raise exc
pypiper.exceptions.SubprocessError: Subprocess returned nonzero result. Check above output for details

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