Error during running umi_tools

Question

[baffiak1902]

Hello,

I'm trying to run umi_tools, but everytime it's finish with error:

Traceback (most recent call last):   File "/usr/local/bin/umi_tools", line 11, in <module>
    load_entry_point('umi-tools==0.5.3', 'console_scripts', 'umi_tools')()   File "/usr/local/lib/python2.7/dist-packages/umi_tools/umi_tools.py", line 59, in main
    module.main(sys.argv)   File "/usr/local/lib/python2.7/dist-packages/umi_tools/count.py", line 110, in main
    for bundle, key, status in bundle_iterator(inreads):   File "/usr/local/lib/python2.7/dist-packages/umi_tools/umi_methods.py", line 1412, in __call__
    self.current_chr = read.reference_name AttributeError: 'csamtools.AlignedRead' object has no attribute 'reference_name'

I'm using STAR version 2.5.2b, featureCounts v1.6.0 and umitools version 0.5.3

Thanks

Answer 1

[smithtomsean]

Late reply but can you try updating to latest version of pysam (and umi_tools since we're now on v0.5.4). I suspect this is due to pysam version. E.g see here: https://github.com/hall-lab/svtyper/issues/12