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4.2 years ago
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I'm having troubles running Blobtools bamfilter ( https://blobtools.readme.io/docs/bamfilter ). I sorted my bam file by name using
samtools sort -n reads.bam > reads.sorted.bam, and provided a list of contigs to include (file shown below):
898 903 405
When I try to run it using
python ./lib/blobtools.py bamfilter -i contigs.txt -u -b reads.sorted.bam I keep getting this error:
Traceback (most recent call last): File "/project/6019012/mat/blobtools-1.0.1/lib/bamfilter.py", line 64, in <module> main() File "/project/6019012/mat/blobtools-1.0.1/lib/bamfilter.py", line 56, in main BtIO.parseBamForFilter(bam_f, include_unmapped, out_f, sequence_list, None, gzip, do_sort, keep_sorted, sort_threads) File "/project/6019012/mat/blobtools-1.0.1/lib/BtIO.py", line 316, in parseBamForFilter runCmd(command=command, wait=True) File "/project/6019012/mat/blobtools-1.0.1/lib/BtIO.py", line 159, in runCmd bufsize=-1) # buffersize of system File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/subprocess.py", line 390, in __init__ errread, errwrite) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/subprocess.py", line 1025, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
Any help with this error is appreciated..thank you.
are you sure, that you are in the same folder where
Yup, 100% sure about that.
Have you checked you can access the external cvmfs files it seems to request accessing from the command line ?
Can you access be ping/web or similar ? Have not worked with cvmfs yet at all.
Heres a web link on what it is if you're unsure: https://cernvm.cern.ch/portal/filesystem