search

HadrienG / InSilicoSeq

:rocket: A sequencing simulator
https://insilicoseq.readthedocs.io
MIT License
176 stars 32 forks source link

iss util fails to remove tmp files when using multiple genomes if chromosomes have the same names #205

Closed sylvainschmitt closed 3 years ago

sylvainschmitt commented 3 years ago

Hi,

Thank you for the nice tool. I'm running the version 1.5.2 using your docker image in a snakemake and singularity workflow. Everything works great until I used two genomes with the option --genomes. As soon as I use more than one genome, iss util fails to remove the temporary file corresponding to the R1 reads:

INFO:iss.util:Cleaning up

ERROR:iss.util:Could not read temporary file: results/test/read.iss.tmp.Qrob_Chr01.0_R1.fastq

ERROR:iss.util:You may have to remove temporary files manually

This is only a temporary file issue, but it stop my snakemake workflow which is problematic. A simple fix is to merge the two genomes manually before using insilicoseq. Nevertheless, I thought I report the bug in case it was not fixed in the last version. It may be related to #143 .

Best,

Sylvain

sylvainschmitt commented 3 years ago

Hello again,

Sorry but I got the origin of the error. When you are using multiple genomes iss util fails to clean files if the names of the chromosomes are the same in the two genomes, which is logical. But maybe an earlier test could catch this error.

Thanks again for the nice tool.

HadrienG commented 3 years ago

Hi,

Thanks for reporting this and for finding the root cause of the problem! I'll try to address this in the next release.

Best, Hadrien.