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  • macs2 -- peak calling error on non-model genome

    Hi there,

    I'm attempting to use macs2 (v 2.0.10 20120605 (tag:alpha)) to call peaks from a ChIP-seq experiment on a non-model organism (sea star).

    Whenever I call this:

    macs2 callpeak -t ip.bam -c inp.bam -f BAM -g 8e+8 --bw 250 -m 10 30 -p 1e-5 --to-large -n TbrChIP-20140729

    macs runs through reading the tags and begins building the peak model. However, it seems to get stuck at the same place each time and throws the following exception:
    Traceback (most recent call last):
    File "/Library/Frameworks/Python.framework/Versions/2.7/bin/macs2", line 337, in <module>
    main()
    File "/Library/Frameworks/Python.framework/Versions/2.7/bin/macs2", line 54, in main
    run( args )
    File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MACS2/callpeak.py", line 249, in run
    peakdetect.call_peaks()
    File "cPeakDetect.pyx", line 224, in MACS2.cPeakDetect.PeakDetect.call_peaks (MACS2/cPeakDetect.c:1703)
    File "cPeakDetect.pyx", line 340, in MACS2.cPeakDetect.PeakDetect.__call_peaks_w_control (MACS2/cPeakDetect.c:3248)
    File "cPileup.pyx", line 72, in MACS2.cPileup.unified_pileup_bdg (MACS2/cPileup.c:1845)
    File "cPileup.pyx", line 136, in MACS2.cPileup.pileup_bdg_se (MACS2/cPileup.c:2279)
    File "cFixWidthTrack.pyx", line 138, in MACS2.IO.cFixWidthTrack.FWTrackIII.get_locations_by_chr (MACS2/IO/cFixWidthTrack.c:2516)
    Exception: No such chromosome name (Scaffold17961) in TrackI object!

    It seems that macs can't find the chromosome (scaffold) named Scaffold17961. I checked and it appears in both the original fasta and the bowtie index I built prior to mapping. Any ideas about how I might be able to get around this issue?

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