Dear All,


I get the following errors when I try to Convert BAM to BigWig




Traceback (most recent call last):
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py",
 line 103, in <module>
    main(*args, **kwargs)
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py",
 line 48, in main
    convert_to_graph(bam_file, split, config, temp_handle)
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py",
 line 76, in convert_to_graph
    subprocess.check_call(cl, stdout=out_handle)
  File "/usr/lib/python2.7/subprocess.py", line 535, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python2.7/subprocess.py", line 522, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory


The tool produced the following additional output:


Have 93 references
Calculating coverage...

or 


Fatal error: Exit code 1 ()
bedtools: 
/galaxy-central/tool_deps/ucsc_tools/312/iuc/package_ucsc_tools_312/2d6bafd63401/lib/libstdc++.so.6:
 version `GLIBCXX_3.4.15' not found (required by bedtools)
needLargeMem: trying to allocate 0 bytes (limit: 100000000000)
Traceback (most recent call last):
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
 line 122, in <module>
    main(*args, **kwargs)
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
 line 57, in main
    convert_to_bigwig(temp_file, sizes, config, outfile)
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py",
 line 104, in convert_to_bigwig
    subprocess.check_call(cl)
  File 
"/galaxy-central/tool_deps/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/subprocess.py",
 line 540, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bedGraphToBigWig', '/tmp/tmp2F67r6', 
'/export/galaxy-central/database/files/003/dataset_3116-sizes.txt', 
'/export/galaxy-central/database/files/003/dataset_3116.dat']' returned 
non-zero exit status 255


The tool produced the following additional output:


Have 93 references
Calculating coverage...
Converting 0 MB graph file to bigwig..

depending what version of the tool i am using.



Any idea what this can be?



I am using the latest Docker-galaxy-stable version (16.04) but I think this is 
not related to docker. All tools are updated.



Thank you very much for your help,



Philipp





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