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Error when running Freebayes: (galaxy-18.01) #1884

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zipho opened this issue May 15, 2018 · 3 comments
Open

Error when running Freebayes: (galaxy-18.01) #1884

zipho opened this issue May 15, 2018 · 3 comments

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@zipho
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zipho commented May 15, 2018

Fatal error: Exit code 2 ()
grep: ./vcf_output/part_.vcf: No such file or directory

The samtools view -H b_0.bam seems to be returning nothing.
@mvdbeek
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mvdbeek commented May 15, 2018 •
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Could you explain this a little more in depth ? What was the input file, what settings have you chosen ? What version of freebayes are you using ?

@zipho
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zipho commented May 15, 2018

The input was picard_MarkDuplicates (bam files) & a reference fasta file.

All settings are default settings.

The version of freebayes is:

Revision: 10:2fb16f415220
from testtoolshed https://testtoolshed.g2.bx.psu.edu/view/devteam/freebayes/2fb16f415220

@mvdbeek
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mvdbeek commented May 16, 2018

Can you reproduce this with a small test file ? What file are you referring to with b_0.bam ?

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@zipho @mvdbeek