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nanoporetech / wub

Tools and software library developed by the ONT Applications group
Mozilla Public License 2.0
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bam_alignment_qc - error #7

Closed Wildstrubu closed 4 years ago

Wildstrubu commented 4 years ago

Hi,

I always get the error at the end of the bam_alignment_qc run. The bam file is sorted and I removed all secondary alignments using "samtools view -F 256 input.bam > output.bam", because I wasn't sure whether that may cause the error as I used minimap2.

Has anyone see this before: Gathering read and error statistics from file: /Data/mini_align/sorted.primary.bam 407037it [39:02, 173.73it/s] File "/user/wub/scripts/bam_alignment_qc.py", line 289, in error_stat_qc(error_stats, plotter, context_sizes, ommit_diagonal=True) File "/user/wub/scripts/bam_alignment_qc.py", line 256, in error_stat_qc if b in nd[cont]: KeyError: 'AAA'

Many thanks for any inputs

pphector commented 4 years ago

I'm also seeing this error frequently and it is very annoying. Unfortunately, it seems like this package is not in active development so I don't think we will receive a reply.

Has anyone figured out what triggers this issue?

bsipos commented 4 years ago

Indeed the package is no longer under active development hence will not investigate the issue more in-depth. However, specifying -n "(1,0)" is worth a try.