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simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
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Excessively large 'err' log file when running with custom phage db (--cp flag) #44

Closed mshamash closed 5 years ago

mshamash commented 5 years ago

Hello,

When running a set of contigs with a --cp flag, the 'err' log file in "logs" folder of working directory ends up being huge (200-400 MB each time), compared to when I run without the --cp flag, it is only a few kb.

The contents of the large 'err' log file is the same line over and over, almost 2 million times:

Use of uninitialized value in concatenation (.) or string at /home/ubuntu/anaconda3/envs/virsorter/lib/site_perl/5.26.2/Bio/SeqUtils.pm line 375.

(/home/ubuntu/anaconda3/ is the path to my anaconda3 installation)

I'm not sure if this is a bug, or if it can be fixed easily, since it takes up a large amount of space when trying to download in bulk all of the output folders from VirSorter. If not, I can try and exclude this folder from downloads, just thought I would bring it up nonetheless.

Best,

Michael

simroux commented 5 years ago

Hi Michael,

This is not a "real" bug, but it is annoying. It's relatively easy to fix, we need to add an "id" to the BioSeq object in the script "Step_first_add_custom_phage_sequence.pl" (l. 163). I just updated the scripts on github, but if you already have a custom install you should be able to adjust the scripts on your side.

Best, Simon

mshamash commented 5 years ago

Hi Simon,

Thanks for the fix. I will update my scripts locally.

Best, Michael