Question: Error during running umi_tools
0
gravatar for baffiak1902
2.4 years ago by
baffiak190210
baffiak190210 wrote:

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

ADD COMMENTlink modified 21 months ago by smithtomsean180 • written 2.4 years ago by baffiak190210
1
gravatar for smithtomsean
21 months ago by
smithtomsean180
United Kingdom
smithtomsean180 wrote:

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

ADD COMMENTlink written 21 months ago by smithtomsean180
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1007 users visited in the last hour