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databio / peppro

A modular, containerized pipeline for PRO-seq data processing
http://peppro.databio.org/
BSD 2-Clause "Simplified" License
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cutadapt related ValueError #65

Closed jpsmith5 closed 4 years ago

jpsmith5 commented 4 years ago

Hmm, the bowtie2_index error was resolved but getting a new error now:

grep 'Reads that were too short:' /home/ww377/peppro_example/test/cutadapt/test_R1_cutadapt.txt | awk '{print $(NF-1)}' Traceback (most recent call last): File "./pipelines/peppro.py", line 3848, in sys.exit(main()) File "./pipelines/peppro.py", line 2227, in main untrimmed_fastq1, outfolder=param.outfolder) File "./pipelines/peppro.py", line 1335, in _process_fastq follow=report_fastq) File "/home/ww377/.local/lib/python3.6/site-packages/pypiper/manager.py", line 795, in run call_follow() File "/home/ww377/.local/lib/python3.6/site-packages/pypiper/manager.py", line 672, in call_follow follow() File "./pipelines/peppro.py", line 1128, in report_fastq ts = float(pm.checkprint(ts_cmd).replace(',','')) ValueError: could not convert string to float:

Originally posted by @wongwic in https://github.com/databio/peppro/issues/62#issuecomment-603879657

jpsmith5 commented 4 years ago

@wongwic I have a couple questions and thoughts in follow-up:

  1. Could you share a cat or a head -n 15 to your /home/ww377/peppro_example/test/cutadapt/test_R1_cutadapt.txt
    • I'm wondering if there has been a change in a recent version of cutadapt that changes the output
    • I'm running on cutadapt version 2.3
  2. Alternatively, it's related to a different version of awk or grep potentially, and it's returning an empty string where I expect a value.
  3. Are you running on Linux it looks like? Or macOS?

I have a feeling this is related to a change in cutadapt where the terminology or column spacing has updated. I'll test the newest version of cutadapt on my end to see if that's the source.

jpsmith5 commented 4 years ago

A ha! Cutadapt v2.9 does not include a "too short" parameter in the output. Let me see if that is now a non-default option, or if they completely eliminated it as a reportable feature.

jpsmith5 commented 4 years ago

Alright @wongwic, this should be addressed in the newest release 0.9.3. Thanks for spotting this.

wongwic commented 4 years ago

Thanks, cutadapt issue has been resolved.