After doing some experimental analysis to debug, I found that the job name was Mg4O4c,try4. Either PBS, linux, or python is adding an escape character (maybe twice). So the variable list shows PBS_O_WORKDIR=/ddn/.../mg404c\\,try4.
When just using the qstat -f -F json command the output looks fine.
sdhutchins
commented
4 years ago
When parsing jobs I came across something interesting. If someone names a job using a coma, then there will be an index error at https://github.com/datasnakes/OrthoEvolution/blob/86a3953ae85a274e499ec7c9173fcd2e78e28d0a/OrthoEvol/Tools/pbs/qstat.py#L386
After doing some experimental analysis to debug, I found that the job name was
Mg4O4c,try4. Either PBS, linux, or python is adding an escape character (maybe twice). So the variable list showsPBS_O_WORKDIR=/ddn/.../mg404c\\,try4.When just using the qstat -f -F json command the output looks fine.