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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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runMACS ERROR #127

Closed mchill2 closed 4 years ago

mchill2 commented 4 years ago

Hello,

Got through to runMACS and then came up with the following error:

runMACS(

  • obj=EC1x.sp[which(EC1x.sp@cluster==1),],
  • output.prefix="Endo_1.1",
  • path.to.snaptools="/home/martinlab/.conda/envs/snapATAC/lib/python2.7/site-packages/snaptools/",
  • path.to.macs="/usr/bin/macs2",
  • gsize="mm",
  • buffer.size=500,
  • num.cores=10,
  • macs.options="--nomodel --shift 37 --ext 73 --qval 1e-2 -B --SPMR --call-summits",
  • tmp.folder=tempdir()
  • ) Epoch: checking input parameters ... Epoch: extracting fragments from each snap files ... sh: 1: /home/martinlab/.conda/envs/snapATAC/lib/python2.7/site-packages/snaptools/: Permission denied cat: /tmp/RtmprHDfTz/file50929778f62.bed.gz: No such file or directory INFO @ Tue, 26 Nov 2019 23:38:19:

    Command line: callpeak -t /tmp/RtmprHDfTz/file50921961618d.bed.gz -f BED -g mm --nomodel --shift 37 --ext 73 --qval 1e-2 -B --SPMR --call-summits -n Endo_1.1

    ARGUMENTS LIST:

    name = Endo_1.1

    format = BED

    ChIP-seq file = ['/tmp/RtmprHDfTz/file50921961618d.bed.gz']

    control file = None

    effective genome size = 1.87e+09

    band width = 300

    model fold = [5, 50]

    qvalue cutoff = 1.00e-02

    Larger dataset will be scaled towards smaller dataset.

    Range for calculating regional lambda is: 10000 bps

    Broad region calling is off

    Searching for subpeak summits is on

    MACS will save fragment pileup signal per million reads

INFO @ Tue, 26 Nov 2019 23:38:19: #1 read tag files... INFO @ Tue, 26 Nov 2019 23:38:19: #1 read treatment tags... Exception ZeroDivisionError: 'integer division or modulo by zero' in 'MACS2.IO.Parser.GenericParser.tsize' ignored INFO @ Tue, 26 Nov 2019 23:38:19: #1 tag size is determined as 0 bps INFO @ Tue, 26 Nov 2019 23:38:19: #1 tag size = 0 INFO @ Tue, 26 Nov 2019 23:38:19: #1 total tags in treatment: 0 INFO @ Tue, 26 Nov 2019 23:38:19: #1 user defined the maximum tags... INFO @ Tue, 26 Nov 2019 23:38:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 26 Nov 2019 23:38:19: #1 tags after filtering in treatment: 0 Traceback (most recent call last): File "/usr/bin/macs2", line 614, in main() File "/usr/bin/macs2", line 56, in main run( args ) File "/usr/lib/python2.7/dist-packages/MACS2/callpeak_cmd.py", line 109, in run info("#1 Redundant rate of treatment: %.2f", float(t0 - t1) / t0) ZeroDivisionError: float division by zero Error in runMACS(obj = EC1x.sp[which(EC1x.sp@cluster == 1), ], output.prefix = "Endo_1.1", : 'MACS' call failed

Any help would be most appreciated.

Best

maggiebr0wn commented 4 years ago

Was this ever resolved? I am running into the same error.