Question: deepTools2: compute matrix error
gravatar for dabates06
3 months ago by
dabates060 wrote:

I get this error when trying to use computeMatrix in the DeepTools2 suite:

Fatal error: Exit code 1 ()
    Traceback (most recent call last):
      File "/cvmfs/", line 11, in <module>
      File "/cvmfs/", line 414, in main
        hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args)
      File "/cvmfs/", line 254, in computeMatrix
        matrix = np.concatenate([r[0] for r in res], axis=0)
    ValueError: need at least one array to concatenate

I'm not sure how to fix this error. I've tried changing many of the parameters. The input was from other tools and follows the DeepTools2 workflow and I didn't have an error in previous steps in the workflow. Any and all help is appreciated.

ADD COMMENTlink modified 3 months ago by Devon Ryan1.9k • written 3 months ago by dabates060

Usually this happens if the BED or GTF file doesn't actually match the bigWig files you're using (e.g., they're from different organisms). Are you using

ADD REPLYlink written 3 months ago by Devon Ryan1.9k

I am using

ADD REPLYlink written 3 months ago by dabates060

If you share that history with "" I'll have a look at why that's happening.

ADD REPLYlink written 3 months ago by Devon Ryan1.9k

I double-checked and the bed file that I obtained from UCSC genome browser and the bamCoverage tool (tool that produces the input for computeMatrix) are using the same C. elegans genome build.

ADD REPLYlink written 3 months ago by dabates060
gravatar for Devon Ryan
3 months ago by
Devon Ryan1.9k
Devon Ryan1.9k wrote:

Your problem is caused by mixing wormbase chromosome names (CHROMOSOME_I, CHROMOSOME_II, etc.) with UCSC chromosome names (chrI, chrII). We wrote deepTools to be able to translate between some chromosome naming systems, but wormbase is weird enough that I never wrote code to support translating it to something more common. Also, the genome version you're using is from 2012, so it's likely that the annotation from UCSC doesn't match it anyway. I suggest doing the following:

  1. Go to ensembl and search for "elegans" in the "filter" box.
  2. Download the "DNA (fasta)" and "Gene sets (GTF)" and upload them to Galaxy.
  3. Redo your alignment against that and use those files with deepTools.

This may seem like extra work, but (A) Ensembl tends to have better quality annotations and (B) a reviewer is likely to complain about you using such an old worm genome version, so you're saving yourself the hassle of dealing with that once you submit your paper.

ADD COMMENTlink written 3 months ago by Devon Ryan1.9k

I will get right on what you suggest. Thanks for your help.

ADD REPLYlink modified 3 months ago • written 3 months ago by dabates060
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