Question: deepTools2: compute matrix error
0
gravatar for dabates06
7 weeks ago by
dabates060
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/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/bin/computeMatrix", line 11, in <module>
        main(args)
      File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/lib/python2.7/site-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 "/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/lib/python2.7/site-packages/deeptools/heatmapper.py", 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 7 weeks ago by Devon Ryan85k • written 7 weeks ago by dabates060

Could you edit your question to include the command you are running? And please use the code button (the button with 101010) to properly format code sections.

ADD REPLYlink written 7 weeks ago by h.mon20k

I'm not sure what you mean by "command you are running". It is probably my inexperience with Galaxy. computeMatrix is the name of the tool in Galaxy. Is this what you mean: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.0.0

ADD REPLYlink written 7 weeks ago by dabates060

You should post this over at Galaxy biostars (biostar clone dedicated for public Galaxy).

Tagging: Devon Ryan in case he can throw some light on this.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by genomax57k

I just posted this on Galaxy biostars. Thank you for pointing out that mistake on my part.

ADD REPLYlink written 7 weeks ago by dabates060

No worries. You are likely to get a speedier response @Galaxy Biostar. @Devon on this forum is one of the developers of deepTools (and knows galaxy well) so that is one option still open.

ADD REPLYlink written 7 weeks ago by genomax57k
1
gravatar for Devon Ryan
7 weeks ago by
Devon Ryan85k
Freiburg, Germany
Devon Ryan85k wrote:

I've replied to this on the Galaxy biostars.

ADD COMMENTlink written 7 weeks ago by Devon Ryan85k
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