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Bloocoo failed on two input files.

I was running Bloocoo-1.0.4 (part of GATB) on two gzip'd fastq files. The documentation says that I can provide the two files in a comma separate list like "read1.fq.gz,read2.fq.gz". This apparently worked at the beginning as I could see a large .h5 file. However, later in the process, I got an error:

EXCEPTION: error opening file: read1.fastq.gz,read2.fastq.gz ()
Command exited with non-zero status 1

Could this be a bug? I have not tried to reproduce the potential issue on smaller examples. Just in case this is a known issue.

gatb
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updated by claire.lemaitre claire.lemaitre • written by lh3 lh3

1 answer

Hi,

This is an error in the documentation, currently Bloocoo is not able to deal with more than one file. In fact, this is only the writing of the output that is not handled, so this is probably easy to implement, and this should be done soon.

Claire

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written by claire.lemaitre claire.lemaitre

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