Question: deeptools computeMatrix error
gravatar for EagleEye
3.8 years ago by
EagleEye6.7k wrote:


I am facing some problem using deeptools (deeptools 2.4.2). Someone please help me solving this issue.


computeMatrix scale-regions -S ./H3K4me2_sorted_nodup.bigWig -R genes.bed --beforeRegionStartLength 2000  --skipZeros -o ./H3K4me2_sorted_nodup_matrix.mat.gz

Input (header):

track type=wiggle_0 name="H3K4me2" description="H3K4me2_sorted_nodup"
variableStep chrom=chr1
56375   3
56385   3
564493  3
564503  5
564513  5
564523  4
564533  4
564543  6


[bwHdrRead] There was an error while reading in the header!
Traceback (most recent call last):
  File "/usr/local/bin/computeMatrix", line 11, in <module>
  File "/usr/local/lib/python2.7/dist-packages/deeptools/", line 414, in main
    hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args)
  File "/usr/local/lib/python2.7/dist-packages/deeptools/", line 235, in computeMatrix
    chromSizes, _ = getScorePerBigWigBin.getChromSizes(score_file_list)
  File "/usr/local/lib/python2.7/dist-packages/deeptools/", line 161, in getChromSizes
    fh =
RuntimeError: Received an error during file opening!
error deeptools • 2.4k views
ADD COMMENTlink modified 3.8 years ago by Devon Ryan97k • written 3.8 years ago by EagleEye6.7k
gravatar for Devon Ryan
3.8 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

That's a wiggle file, not a bigWig file. You'll need to convert it.

ADD COMMENTlink written 3.8 years ago by Devon Ryan97k

Yes, sorry. It is working perfectly. Thanks for the tool (saves lot of time).

ADD REPLYlink written 3.8 years ago by EagleEye6.7k
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