Error while running MACS2 ATAC-seq data

Question

[Benn]

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?

command:

macs2 callpeak -t S2.srt.bam S4.srt.bam S5.srt.bam S8.srt.bam \
-c S3.srt.bam S7.srt.bam S9.srt.bam \
-f BAMPE -g hs -n Mut_vs_Wt -B -q 0.05 --outdir Results --nomodel --shift -100 --extsize 200

error:

Traceback (most recent call last):
  File "/usr/local/bin/macs2", line 5, in <module>
    pkg_resources.run_script('MACS2==2.1.0.20151222', 'macs2')
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 499, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 1235, in run_script
    execfile(script_filename, namespace, namespace)
  File "/usr/local/lib/python2.7/dist-packages/MACS2-2.1.0.20151222-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in <module>
    main()
  File "/usr/local/lib/python2.7/dist-packages/MACS2-2.1.0.20151222-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 56, in main
    run( args )
  File "/usr/local/lib/python2.7/dist-packages/MACS2-2.1.0.20151222-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 261, in run
    peakdetect.call_peaks()
  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!

[ejm32]

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 https://github.com/taoliu/MACS/wiki/Advanced:-Call-peaks-using-MACS2-subcommands

[Benn]

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