Help with bamfilter

Question

[max_19]

Hi all,

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):

contigs.txt

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.

[finswimmer]

Hello,

are you sure, that you are in the same folder where contigx.txt and reads.sorted.bam are located?

fin swimmer

[max_19]

Yup, 100% sure about that.

[colindaven]

Have you checked you can access the external cvmfs files it seems to request accessing from the command line ?

 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

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