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  1. UGENE
  2. UGENE-6380

"Classify Sequences with MetaPhlAn2" workflow element doesn't create a folder for the output files correctly

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: master
    • Fix Version/s: 1.32
    • Component/s: NGS, Workflow
    • Labels:
    • Sprint:
      DEV-32-RELEASE, DEV-33-2
    • Affect Type:
      Userdefined

      Description

      "Classify Sequences with MetaPhlAn2" workflow element always creates a folder for output files inside the workflow output folder, even when one sets specific URLs in parameters "Bowtie2 output file" and "Output file". In case when the output folder doesn't exist MetaPhlAn2 tool fails with the following data in stderr output:

      Warning! Biom python library not detected!
Exporting to biom format will not work!
Help message for read_fastx.py
Traceback (most recent call last):
File "/Applications/U-1.32.0-full-rc2.app/Contents/MacOS/tools/metaphlan2-2.7.7/metaphlan2.py", line 1565, in 
metaphlan2()
File "/Applications/U-1.32.0-full-rc2.app/Contents/MacOS/tools/metaphlan2-2.7.7/metaphlan2.py", line 1482, in metaphlan2
with (open(pars['output'],"w") if pars['output'] else sys.stdout) as outf:
IOError: [Errno 2] No such file or directory: '/Users/atiunov/root/qwe/22 22/qweasd/qweasd'

      The following should be done:

      1. Do not create unnecessary folder in the workflow output folder.
      2. Create a folder for the output files.

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            Assignee:
            dsukhomlinov Dmitrii Sukhomlinov
            Reporter:
            atiunov Aleksey Tiunov [X] (Inactive)
            Assigned Tester:
            Kirill Rasputin
            Watchers:
            2 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: