QuASAR-QC output folder

[Phlya]

QuASAR-QC always prepends $HOME to the path of the specified folder, i.e. I ran

3DChromatin_ReplicateQC qc --running_mode sge --metadata_samples QCRep_metadata.samples --outdir ./output --methods QuASAR-QC

but it tried to save to

/home/s1529682/./output/scripts/QuASAR-QC/WT-1/WT-1.QuASAR-QC.sh.o

And this folder structure of course doesn't exist, and the job fails.

[oursu]

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.

[Phlya]

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...

[Phlya]

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:                  s1529682@login03.ecdf.ed.ac.uk
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?..