computeMatrix error: [pyBwOpen] bw is NULL!

Question

[bp22]

Hi all,

I am trying to run computeMatrix in DeepTools and getting the following error:

[bwHdrRead] There was an error while reading in the header!
[pyBwOpen] bw is NULL!
Traceback (most recent call last):
File "/Users/bp/opt/anaconda3/bin/computeMatrix", line 8, in <module>
sys.exit(main())
File "/Users/bp/opt/anaconda3/lib/python3.9/site-packages/deeptools/computeMatrix.py", line 428, in main
hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args)
File "/Users/bp/opt/anaconda3/lib/python3.9/site-packages/deeptools/heatmapper.py", line 251, in computeMatrix
chromSizes, _ = getScorePerBigWigBin.getChromSizes(score_file_list)
File "/Users/bp/opt/anaconda3/lib/python3.9/site-packages/deeptools/getScorePerBigWigBin.py", line 158, in getChromSizes
fh = pyBigWig.open(fname)
RuntimeError: Received an error during file opening!

I have tried multiple different options discussed such as updating pybigwig and others but to no success in solving this issue.

The bigWig files were generated from BAM files using either bamCoverage or bamCompare from deeptools. I have run computeMatrix before using bigWig files generated in the same manner and have never had any issue.

Any ideas on why I am encountering this issue would be highly helpful.

Thank you.

Best, BP

[rfran010]

Are you sure there wasn't an error during bigwig generation, like out of memory? Can you use the bigWigToBedGraph binary to convert to bedgraph? If that doesn't work either, then you can focus on any issues with the bigwig file itself.