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CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets
MIT License
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umi_tools dedup ValueError: max() arg is an empty sequence #514

Closed prmunn closed 2 years ago

prmunn commented 2 years ago

I'm getting the following error: Traceback (most recent call last): File "/programs/UMI-tools/bin/umi_tools", line 8, in sys.exit(main()) File "/programs/UMI-tools/lib64/python3.6/site-packages/umi_tools/umi_tools.py", line 61, in main module.main(sys.argv) File "/programs/UMI-tools/lib64/python3.6/site-packages/umi_tools/dedup.py", line 415, in main post_cluster_stats_null]))) ValueError: max() arg is an empty sequence

When I execute the following command: umi_tools dedup --paired \ --per-cell \ --no-sort-output \ --unmapped-reads=discard \ --chimeric-pairs=discard \ --unpaired-reads=discard \ --output-stats=Barnyard1.dedup \ -L Barnyard1.dedup.log \ -I Barnyard1.noBlacklist.bam \ -S Barnyard1.DEDUP_unsorted.bam

Any idea what would cause this?

prmunn commented 2 years ago

Looks like this was my fault - I had a bug in my code upstream of this when I was creating the input bam file. Sorry. Closing the issue.