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xml.etree.ElementTree.ParseError #13

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GiulioCentorame opened this issue Oct 27, 2022 · 0 comments
Open

xml.etree.ElementTree.ParseError #13

GiulioCentorame opened this issue Oct 27, 2022 · 0 comments

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@GiulioCentorame
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GiulioCentorame commented Oct 27, 2022

I am trying to run this profile on our pbspro cluster, but I am getting the following error at every submission:

  Traceback (most recent call last):
  File "/home/user/.config/snakemake/pbs-torque/pbs-status.py", line 12, in <module>
    xmldoc = ET.ElementTree(ET.fromstring(res.stdout.decode())).getroot()
  File "/home/user/mambaforge/envs/snakemake/lib/python3.10/xml/etree/ElementTree.py", line 1342, in XML
    parser.feed(text)
xml.etree.ElementTree.ParseError: syntax error: line 1, column 0

Edit: apparently my cluster uses nonstandard names, so xmldoc fails as it cannot find a job in the format jobid (e.g., in my case it's jobid.something). I don't know if there is an easy fix for this, as it would need to match the specific cluster specs

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