Re: [macs-announscement] MACS2 callpeak fatal error

[Tao Liu]

No such file or directory: 'chip_CR4D_2.bed'

File can't be found. Check if your path is correct.

Best,

Tao Liu

--

Assistant Professor
Deptartment of Biochemistry
SUNY at Buffalo
NY State Center of Excellence in Bioinformatics & Life Sciences

B2-163 COEBLS
(O) 716-829-2749
tl...@buffalo.edu

Mailing address:
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On Mar 7, 2013, at 4:04 AM, Jose Luis Lavin <jol...@gmail.com> wrote:

Hello everybody,

I've been trying to use MACS2 as peak caller following the guidelines for ChIP-seq analysis publiched by the ENCODE project. But I get the same error whether if I used the bed format or the tagAlign format as input ( I've tried with .gz compressed files and uncompressed files also).
Here are the details for this issue:

Command used for peak calling :

 macs2 callpeak -t chip_CR4D_2.bed -c controlSampleRep0.bed -f BED -n chip_CR4D_2\_VS_controlSample_Rep0 -g mm -p 1e-3 --to-large

Error I get:

Traceback (most recent call last):
  File "/opt/python/python-2.7.3/bin/macs2", line 362, in <module>
    main()
  File "/opt/python/python-2.7.3/bin/macs2", line 45, in main
    run( args )
  File "/opt/macs/MACS-2.0.10/lib/python2.7/site-packages/MACS2/callpeak.py", line 70, in run
    else:       (treat, control) = load_tag_files_options  (options)
  File "/opt/macs/MACS-2.0.10/lib/python2.7/site-packages/MACS2/callpeak.py", line 350, in load_tag_files_options
    tp = options.parser(options.tfile[0])
  File "cParser.pyx", line 147, in MACS2.IO.cParser.GenericParser.__init__ (MACS2/IO/cParser.c:2625)
  File "/opt/python/python-2.7.3/lib/python2.7/gzip.py", line 34, in open
    return GzipFile(filename, mode, compresslevel)
  File "/opt/python/python-2.7.3/lib/python2.7/gzip.py", line 89, in __init__
    fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
IOError: [Errno 2] No such file or directory: 'chip_CR4D_2.bed'

Thanks in advance for your help.

Best wishes

JL

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[Jose Luis Lavin]

Sorry Tao, I pasted the wrong error here. I've already got multiple errors (not counting the ones like this I posted previously) and most of them (seem to me) referred to MACS2 processing. I had python v.2.7.3 and went back to v2.7.2 (with the numpy v.1.7.0 and cython v.0.14.1).

I'll paste the latest error here, and let's see if you can help, a newbie like me, to fix/avoid it ;)

Traceback (most recent call last):
  File "/opt/python/python-2.7.2/bin/macs2", line 362, in <module>
    main()
  File "/opt/python/python-2.7.2/bin/macs2", line 45, in main
    run( args )
  File "/opt/python/python-2.7.2/lib/python2.7/site-packages/MACS2/callpeak.py", line 100, in run
    treat.separate_dups(treatment_max_dup_tags) # changed 5-29
  File "cFixWidthTrack.pyx", line 207, in MACS2.IO.cFixWidthTrack.FWTrackIII.separate_dups (MACS2/IO/cFixWidthTrack.c:5318)
  File "cFixWidthTrack.pyx", line 325, in MACS2.IO.cFixWidthTrack.FWTrackIII.separate_dups (MACS2/IO/cFixWidthTrack.c:5191)
UnboundLocalError: local variable 'dup_minus' referenced before assignment

Thanks again for your kind answer

JL

[Tao Liu]

Hi Jose,

This looks familiar.  MACS2 (2012-09-14) can't tolerate the case when there is no tag in one stand of chromosome. I don't believe ENCODE data has such problem … Anyway, it has been fixed last November, so now MACS2 can process such weird datasets. You can update your code to newest version at github or at pypi. Sorry about the inconvenience. 

Best,

Tao Liu

--

Assistant Professor
Deptartment of Biochemistry
SUNY at Buffalo
NY State Center of Excellence in Bioinformatics & Life Sciences

B2-163 COEBLS
(O) 716-829-2749
tl...@buffalo.edu

Mailing address:
SUNY at Buffalo-COEBLS
701 Ellicott St, B2-163
Buffalo, NY 14203-1221

[Jose Luis Lavin]

Thank you Tao,
 I downloaded the last code (added a few days ago, I hope that's the last update) and it seems to work even with this dataset.

;)

Best wishes

JL