IRescue error: Traceback (most recent call last): File "/apps/software/gcc-12.1.0/python/3.10.5/bin/irescue", line 8, in <module> sys.exit(main()) about irescue HOT 3 CLOSED

Hi @tcmartinez,
sorry for the delay.

You're getting the same error as #1, however that was fixed.
I noticed that, sometimes, samtools indexes are corrupted (i.e. they do not allow to query the BAM file), causing the same error again even with IRescue 1.0.3. It happens quite randomly, so I couldn't fix it yet.

Please, try this:

• delete or move BAM's index, to let IRescue build the index again with samtools. Alternatively, re-build the index yourself (then check if it works by running samtools view Aligned.sortedByCoord.out.bam chr1 | head).
• execute IRescue again, but add the parameter -v to get more info about the run.
• can you also double check that your whitelist file contains the barcodes indicated with the "CB" tag in the BAM file? It suffices to check just one barcode.

Thanks
B

from irescue.

Thank you so much for your help . The issue was with my whitelist.

from irescue.

No problem, I'm glad you solved it

from irescue.