Entering edit mode
8.0 years ago
EagleEye
7.6k
Hello,
I am facing some problem using deeptools (deeptools 2.4.2). Someone please help me solving this issue.
Command:
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
Error:
[bwHdrRead] There was an error while reading in the header!
Traceback (most recent call last):
File "/usr/local/bin/computeMatrix", line 11, in <module>
main(args)
File "/usr/local/lib/python2.7/dist-packages/deeptools/computeMatrix.py", 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/heatmapper.py", line 235, in computeMatrix
chromSizes, _ = getScorePerBigWigBin.getChromSizes(score_file_list)
File "/usr/local/lib/python2.7/dist-packages/deeptools/getScorePerBigWigBin.py", line 161, in getChromSizes
fh = pyBigWig.open(fname)
RuntimeError: Received an error during file opening!
Yes, sorry. It is working perfectly. Thanks for the tool (saves lot of time).