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--nocorr option fails at pilon step. #33

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Slugger70 opened this issue Sep 5, 2017 · 1 comment
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--nocorr option fails at pilon step. #33

Slugger70 opened this issue Sep 5, 2017 · 1 comment
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Slugger70 commented Sep 5, 2017 •
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When running with --nocorr option, shovill 0.7.1 fails and returns the following error:

User supplied --nocorr, so not correcting contigs.
read_file 'pilon.changes' - sysopen: No such file or directory at /home/ubuntu/miniconda3/bin/shovill line 296.

Commandline used:
shovill --outdir out_nocorr --R1 mutant_R1.fastq --R2 mutant_R2.fastq --nocorr --ram 6
@tseemann tseemann self-assigned this Sep 7, 2017
@tseemann tseemann added the bug label Sep 7, 2017
@tseemann tseemann added this to the Release 1.0 milestone Sep 7, 2017
tseemann added a commit that referenced this issue Sep 7, 2017
@tseemann
Issue #33 | only parse pilon output if it was run
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tseemann commented Sep 7, 2017

Nice find! Thank you. Fixed.

@tseemann tseemann closed this as completed Sep 7, 2017
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