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Space in file name causing failure for workflow when loading genome. #82

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elyons opened this issue Sep 2, 2020 · 0 comments
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elyons commented Sep 2, 2020

CoGe's reported error:

######################### Sorting FASTA file Job: /opt/apache2/coge/scripts/sort_fasta.pl Pa_scaffold 0_7.fa > Pa_scaffold 0_7.fa.sorted Submitted at: 02/09/20 at 01:19:13AM Completed at: 02/09/20 at 01:19:14AM Execution time: 0.026153 sec Assigned to task: 16089 Return status: 2 Expected outputs: /scratch/coge/tmp/staging/twoehner85/272865/Pa_scaffold 0_7.fa.sorted Command Output: "Could not build fai index Pa_scaffold.fai\nCouldn't create index file at /opt/apache2/coge/scripts/sort_fasta.pl line

Note: file name is "Pa_scaffold 0_7.fa"

I have cached this file in my data store for debugging purposes.

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