Question: Bloocoo failed on two input files.
gravatar for lh3
2.7 years ago by
United States
lh330k wrote:

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 • 711 views
ADD COMMENTlink modified 2.7 years ago by claire.lemaitre100 • written 2.7 years ago by lh330k
gravatar for claire.lemaitre
2.7 years ago by
claire.lemaitre100 wrote:


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.


ADD COMMENTlink written 2.7 years ago by claire.lemaitre100
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