MACS2 error: No such file or directory: 'None'

[mads.b...@gmail.com]

Hi there:

Tried to do MACS2 peak calling on a ChIP-seq dataset bam format, however got the error message below. Have tried several different datasets and get the same error each time. 

What should I do to successfully call the peaks, am I using some wrong settings?

Thanks for the help,

Mads

INFO  @ Wed, 02 Sep 2015 07:23:03: #1.2 read input tags... 
Traceback (most recent call last):
  File "/usr/local/bin/macs2", line 559, in <module>
    main()
  File "/usr/local/bin/macs2", line 56, in main
    run( args )
  File "/usr/local/lib/python2.7/dist-packages/MACS2/callpeak.py", line 72, in run
    else:       (treat, control) = load_tag_files_options  (options)
  File "/usr/local/lib/python2.7/dist-packages/MACS2/callpeak.py", line 404, in load_tag_files_options
    control = options.parser(options.cfile[0], buffer_size=options.buffer_size).build_fwtrack()
  File "cParser.pyx", line 665, in MACS2.IO.cParser.BAMParser.__init__ (MACS2/IO/cParser.c:8380)
  File "/usr/lib/python2.7/gzip.py", line 34, in open
    return GzipFile(filename, mode, compresslevel)
  File "/usr/lib/python2.7/gzip.py", line 94, in __init__
    fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
IOError: [Errno 2] No such file or directory: 'None'

[Jian Ma]

Hi Mads,

The input bam file might be truncated. You may need to try the samtools http://www.htslib.org/doc/samtools.html to see if it can read the bam file.

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best，

Jian Ma,