Ambiguous error message when SAM file contains no UMI in htseq-count-umified
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jarondl commented
If one runs htseq-count-umified
with umi=true
, but without UMIs in the SAM file, the error message is quite unclear:
Error occured when processing SAM input (line 97460 of file SAMFILE):
Traceback (most recent call last):
File "/illumina1/YanaiLab/new_fs/tools/bin/pijpleiding_stable", line 129, in <module>
main(args.config_file)
File "/illumina1/YanaiLab/new_fs/tools/bin/pijpleiding_stable", line 93, in main
segment(**parameters)
File "/illumina1/YanaiLab/new_fs/tools/pipeline_stable/htseq_wrapper.py", line 82, in main
results = pool.map(run_cmd, cmds)
File "/usr/lib/python2.7/multiprocessing/pool.py", line 250, in map
return self.map_async(func, iterable, chunksize).get()
File "/usr/lib/python2.7/multiprocessing/pool.py", line 554, in get
raise self._value
AttributeError: 'NoneType' object has no attribute 'group'
That is because the relevant code block ( https://github.com/yanailab/CEL-Seq-pipeline/blob/stable/htseq_count_umified.py#L50 ) assumes a umi is always matched.
A better error message should apear.