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NickSto / bfx

Generally useful bioinformatics scripts
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RuntimeError in trimmer.py in Galaxy #2

Open NickSto opened 4 years ago

NickSto commented 4 years ago

@afgane reported that the Sequence Content Trimmer Galaxy tool raises a RuntimeError when executed in Galaxy, but not when executed in the same Docker container, but outside of Galaxy. The error does not seem to affect the output - it was identical to an output that didn't come with the error.

This is the traceback. The input was the data 10 & 11 from https://usegalaxy.org/u/nstoler/h/du-novo-gtn-tutorial. His options were as in the following command line: $ python trimmer.py no10 no11 out1 out2 -f fastq -b ACGT -t 0.2 -w 10 --invert -m 50

Traceback (most recent call last):
  File "/galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/nick/sequence_content_trimmer/7f170cb06e2e/sequence_content_trimmer/getreads.py", line 130, in parser
    raise StopIteration
StopIteration

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/nick/sequence_content_trimmer/7f170cb06e2e/sequence_content_trimmer/trimmer.py", line 220, in <module>
    sys.exit(main(sys.argv))
  File "/galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/nick/sequence_content_trimmer/7f170cb06e2e/sequence_content_trimmer/trimmer.py", line 89, in main
    trim_reads(file1_parser, file2_parser, args.outfile1, args.outfile2, filetype1, filetype2,
  File "/galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/nick/sequence_content_trimmer/7f170cb06e2e/sequence_content_trimmer/trimmer.py", line 105, in trim_reads
    read1 = next(file1_parser)
RuntimeError: generator raised StopIteration
NickSto commented 4 years ago

The error does not appear when I ran it on usegalaxy.org with the same inputs and options. - The tool was at Galaxy Version 0.1