search

bcgsc / mavis

Merging, Annotation, Validation, and Illustration of Structural variants
http://mavis.bcgsc.ca
GNU General Public License v3.0
72 stars 14 forks source link

Error in sge parsing #175

Closed calchoo closed 5 years ago

calchoo commented 5 years ago

From Alexander Fortuna

Dear Mavis Team,

I have been working to run MAVIS on our HPC which runs with SGE and have been running into the issue of parsing qstat content. I imagine our qstat content is formatted differently then it is at BCGSC. I have attached my qstat output as well as the error message. I am using mavis 2.2.0 and I am trying to validate star fusion transcriptome fusion transcripts.

In the attached text file I included the tracebacks for two errors. The first I solved by altering the parse_qstat

lines = [l for l in content.split('\n') if l.strip() and not l.startswith('=')]

I have been working independently to alter the parse_qstat portion to solve error #2 but I am wondering if you had another suggestion. I would appreciate any insight.

Kind Regards, Alexander Fortuna

calchoo commented 5 years ago

@alexjfortuna, I've released a new version with the fix for qstat, could you test it out? There are still some improvements I would like to add for error handling on SGE but I will be working on including these in a future release

alexjfortuna commented 5 years ago

@calchoo I am no longer receiving SGE errors when MAVIS parses qstat. Thank you!