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databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
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pypiper.exceptions.SubprocessError: Subprocess returned nonzero result. #270

Closed zhongzheng1999 closed 5 months ago

zhongzheng1999 commented 5 months ago

test1_rCRSd_bt_aln_summary.log

PEPATAC_test1.log

I hope this message finds you well. I am reaching out to report an issue I encountered while running the PEPATAC test file using the command "looper run examples/test_project/test_config.yaml." The error message I received is as follows:

Pipeline failed at: (01-30 18:23:32) elapsed: 1.0 TIME

Total time: 0:00:13 Failure reason: Subprocess returned nonzero result. Check above output for details Traceback (most recent call last): File "/home/u2204084007/biosoft/pepatac-0.11.2/pipelines/pepatac.py", line 2779, in sys.exit(main()) File "/home/u2204084007/biosoft/pepatac-0.11.2/pipelines/pepatac.py", line 971, in main unmap_fq1, unmap_fq2 = _align( File "/home/u2204084007/biosoft/pepatac-0.11.2/pipelines/pepatac.py", line 387, in _align pm.run(cmd, [summary_file, out_fastq_r2_gz]) File "/home/u2204084007/mambaforge/envs/pepatac/lib/python3.9/site-packages/pypiper/manager.py", line 1083, in run process_return_code, local_maxmem = self.callprint( File "/home/u2204084007/mambaforge/envs/pepatac/lib/python3.9/site-packages/pypiper/manager.py", line 1352, in callprint self._triage_error(SubprocessError(msg), nofail) File "/home/u2204084007/mambaforge/envs/pepatac/lib/python3.9/site-packages/pypiper/manager.py", line 2575, in _triage_error self.fail_pipeline(e) File "/home/u2204084007/mambaforge/envs/pepatac/lib/python3.9/site-packages/pypiper/manager.py", line 2045, in fail_pipeline raise exc pypiper.exceptions.SubprocessError: Subprocess returned nonzero result. Check above output for details

I have uploaded the corresponding log file for your reference.

Upon further investigation, I suspect the error may be related to prealignments. In the log file "test1_rCRSd_bt_aln_summary.log" within the "prealignments" folder, the following message is present:

"default/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4" does not exist or is not a Bowtie 2 index.

However, I want to highlight that I have executed the following commands:

refgenie pull rCRSd/bowtie2_index
refgenie seek rCRSd/bowtie2_index.dir

Despite these commands being run, it seems that there is an issue with the Bowtie 2 index. I would appreciate your assistance in resolving this matter. If you require additional information or logs, please let me know, and I will promptly provide them.

Thank you for your attention to this matter.

zhongzheng1999 commented 5 months ago

I must admit, I made a somewhat amusing mistake that left me both laughing and crying. I naively believed that the refgenie seek command would automatically update the content of the bowtie2 index location in the yaml file. However, it turns out that I need to manually modify this location in the yaml file. Lesson learned!