Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • MACS "Exception: Can't detect format!" error

    I'm running MACS on some .bam files, and I'm coming across this error on one particular .bam file (but not all .bam files) and I'm not sure what to do about it:

    INFO @ Fri, 05 Jun 2015 11:14:58:
    # ARGUMENTS LIST:
    # name = 1487
    # format = AUTO
    # ChIP-seq file = 1487_filtered.bam
    # control file = 1580_input_filtered2.bam
    # effective genome size = 2.70e+09
    # band width = 300
    # model fold = 10,30
    # pvalue cutoff = 1.00e-05
    # Large dataset will be scaled towards smaller dataset.
    # Range for calculating regional lambda is: 1000 bps and 10000 bps

    INFO @ Fri, 05 Jun 2015 11:14:58: #1 read tag files...
    INFO @ Fri, 05 Jun 2015 11:14:58: #1 read treatment tags...
    Traceback (most recent call last):
    File "/usr/local/bin/macs14", line 5, in <module>
    pkg_resources.run_script('MACS==1.4.2', 'macs14')
    File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 489, in run_script
    self.require(requires)[0].run_script(script_name, ns)
    File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 1214, in run_script
    exec script_code in namespace, namespace
    File "/Library/Python/2.7/site-packages/MACS-1.4.2-py2.7.egg/EGG-INFO/scripts/macs14", line 366, in <module>

    File "/Library/Python/2.7/site-packages/MACS-1.4.2-py2.7.egg/EGG-INFO/scripts/macs14", line 60, in main

    File "/Library/Python/2.7/site-packages/MACS-1.4.2-py2.7.egg/EGG-INFO/scripts/macs14", line 333, in load_tag_files_options

    File "build/bdist.macosx-10.9-intel/egg/MACS14/IO/Parser.py", line 60, in guess_parser
    Exception: Can't detect format!


    Other forum postings suggest that I should patch Macs14, as specified in http://ashishagarwal.org/2011/03/26/macs14-patch/

    However, the error this patch would fix is not the one I'm dealing with. Has anyone else had this error?

    For reference, here is the script I'm using to run MACS:
    macs14 -t $name1 -c $name2 -g hs -n $name3 -B -S --call-subpeaks

    Uchillama

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X