QuASAR-QC output folder about 3dchromatin_replicateqc HOT 3 OPEN

Hi @Phlya

I am not sure how to help. Does it work if you provide the full path to the output directory rather than a relative one (so--outdir /full/path/to/output, rather than --outdir ./output?

It's strange because I do convert the specified output directory to the full path (https://github.com/kundajelab/genomedisco/blob/master/genomedisco/concordance_utils.py#L126, so I'm confused about why this happens. I might be missing something really basic here, I apologize.

from 3dchromatin_replicateqc.

Specifying full path to the output folder works, thanks.

Does it maybe change the working directory somewhere for some reason, before doing this? If you look at the output file name above, it's actually the qsub output file which it locates to a wrong folder, so it's not a problem with actual output of the programme, but of the qsub script...

from 3dchromatin_replicateqc.

stderr_path_list:           NONE:NONE:./output/scripts/QuASAR-QC/WT-1/WT-1.QuASAR-QC.sh.e
hard resource_list:         h_rt=14400,h_vmem=32G
mail_list:                  [email protected]
notify:                     FALSE
job_name:                   WT-1.QuASAR-QC.sh
stdout_path_list:           NONE:NONE:./output/scripts/QuASAR-QC/WT-1/WT-1.QuASAR-QC.sh.o

This is part of the qstat output about one of these jobs when using a relative path - where do these NONE:NONE: come from?..

from 3dchromatin_replicateqc.