problem with methylation BigWig

[gyanmishra]

Hi,

I generated bigwig file for methylation data to plot average methylation level on set of genomic regions but I am getting the below mentioned error. I am using deeptool 3.5.0 and python 3.7. To generate bigWig coverage file for methylation bed file and used chr, start and end and score (fraction of methylation cytosine at per base) column.

My bed file looks like this

chr1 3000678 3000679 0.2 chr1 3001310 3001311 0.4 chr1 3002046 3002047 0.333333333333333 chr1 3003445 3003446 0.333333333333333 chr1 3003991 3003992 0.333333333333333 chr1 3004152 3004153 0.5 chr1 3005126 3005127 0.5 chr1 3005307 3005308 0.333333333333333 chr1 3005815 3005816 0.333333333333333 chr1 3007568 3007569 0.25

full deepTools command that produces the issue

computeMatrix reference-point  -S  GSM3666121_CA_allchrs.bw GSM3666122_CA_allchrs.bw GSM3666123_CA_allchrs.bw \
           GSM3666124_CA_allchrs.bw GSM3666125_CA_allchrs.bw GSM3666126_CA_allchrs.bw \
       -R DNMT3a.bed --referencePoint center \
       -b 4000 -a 4000 --skipZeros -bs 100  -o DNMT3a.gz

output printed on screen from the command that produced the issue

Traceback (most recent call last):
  File "/cm/shared/apps/deeptools/3.5.0/bin/computeMatrix", line 14, in <module>
    main(args)
  File "/cm/shared/apps/deeptools/3.5.0/lib/python3.7/site-packages/deeptools/computeMatrix.py", line 421, in main
    hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args)
  File "/cm/shared/apps/deeptools/3.5.0/lib/python3.7/site-packages/deeptools/heatmapper.py", line 264, in computeMatrix
    verbose=verbose)
  File "/cm/shared/apps/deeptools/3.5.0/lib/python3.7/site-packages/deeptools/mapReduce.py", line 146, in mapReduce
    res = list(map(func, TASKS))
  File "/cm/shared/apps/deeptools/3.5.0/lib/python3.7/site-packages/deeptools/heatmapper.py", line 174, in compute_sub_matrix_wrapper
    return heatmapper.compute_sub_matrix_worker(*args)
  File "/cm/shared/apps/deeptools/3.5.0/lib/python3.7/site-packages/deeptools/heatmapper.py", line 538, in compute_sub_matrix_worker
    not self.quiet)
  File "/cm/shared/apps/deeptools/3.5.0/lib/python3.7/site-packages/deeptools/heatmapper.py", line 719, in coverage_from_big_wig
    values_array[startIdx:endIdx] = bigwig.values(chrom, start, end)
ValueError: cannot copy sequence with size 0 to array axis with dimension 3915

Thanks Gyan