voila modulize output

[Rotem Zilka]

Hi, 

I’m currently trying to run the voila modulize command and encountered a couple of issues:  

1. In the log file, I see the following error: 
TypeError: SpliceGraphZarr.__init__() missing 1 required positional argument: 'sgc_files' 

2.The files are being created and are not empty, but in cassette.tsv (for example), the sample columns that should contain PSI values are empty.

 Here’s the command I’m running:  

nohup voila modulize \
  "$SGC_FILE" "$PSICOV_FILE" "$SPLICEGRAPH_ZARR" \
  --directory "$output" \
  --nproc 4 \
  --debug-num-genes 1000 \
  --keep-constitutive \
  --debug \
  --overwrite \
  --logger modulize.log > modulize_nohup.out 2>&1 &

Could you please advise on what might be causing these issues or suggest how I can troubleshoot them?

Thanks in advance for your help!

Rotem

[San Jewell]

Hi Rotem,

I generally wasn't able to reproduce this error on the current version of majiq/voila ; however, over the past month since release, there have been a number of bug fixes released already due to good user feedback. If you are not sure, I would recommend reinstalling using the same repository you used previously in order to make sure you are on the latest version. If this error still manifests, could you please post the list of majiq/voila commands in full so I can check if there is a weird situation which might lead to this? You could message me privately in that case if you would like to avoid posting the commands on the board.

Thanks,

-San