Question: Error while running MACS2 ATAC-seq data
gravatar for Benn
3.6 years ago by
Benn8.0k wrote:

Hi Guys,

I am trying to run MACS2 for ATAC-seq data, it worked with a part of my bam files, but with another set of bam files I get this error... Anyone ideas what's wrong?


macs2 callpeak -t \
-c \
-f BAMPE -g hs -n Mut_vs_Wt -B -q 0.05 --outdir Results --nomodel --shift -100 --extsize 200


Traceback (most recent call last):
  File "/usr/local/bin/macs2", line 5, in <module>
    pkg_resources.run_script('MACS2==', 'macs2')
  File "/usr/lib/python2.7/dist-packages/", line 499, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/lib/python2.7/dist-packages/", line 1235, in run_script
    execfile(script_filename, namespace, namespace)
  File "/usr/local/lib/python2.7/dist-packages/MACS2-", line 614, in <module>
  File "/usr/local/lib/python2.7/dist-packages/MACS2-", line 56, in main
    run( args )
  File "/usr/local/lib/python2.7/dist-packages/MACS2-", line 261, in run
  File "MACS2/PeakDetect.pyx", line 105, in MACS2.PeakDetect.PeakDetect.call_peaks (MACS2/PeakDetect.c:1632)
  File "MACS2/PeakDetect.pyx", line 177, in MACS2.PeakDetect.PeakDetect.__call_peaks_w_control (MACS2/PeakDetect.c:2163)
AssertionError: slocal can't be smaller than d!
macs2 atac • 1.6k views
ADD COMMENTlink written 3.6 years ago by Benn8.0k

It's telling you on the last line. Your slocal (size of local background correction) parameter is smaller than d (estimated fragment size). This may help

ADD REPLYlink written 3.6 years ago by ejm32440

Thanks for the link, the error message was too cryptic for me I guess...

ADD REPLYlink written 3.6 years ago by Benn8.0k
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