Deeptools: computeMatrix - Traceback

Question

[ATpoint]

Hello, I aim to run deeptools computeMatrix -reference-point with settings that I've used multiple times for different data sets. Still, in this case, I get the following error:

Traceback (most recent call last):
  File "/Users/atoenges/anaconda/bin/computeMatrix", line 7, in <module>
    main()
  File "/Users/atoenges/anaconda/lib/python2.7/site-packages/deeptools/computeMatrix.py", line 378, in main
    hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args)
  File "/Users/atoenges/anaconda/lib/python2.7/site-packages/deeptools/heatmapper.py", line 247, in computeMatrix
    keepExons=keepExons)
  File "/Users/atoenges/anaconda/lib/python2.7/site-packages/deeptools/mapReduce.py", line 142, in mapReduce
    res = pool.map_async(func, TASKS).get(9999999)
  File "/Users/atoenges/anaconda/lib/python2.7/multiprocessing/pool.py", line 567, in get
    raise self._value
IndexError: list index out of range

I noticed then that it did not occur when I removed all entries from the bed file that belong to chr1. Initially, I suspected that the some chr1 entries contain out-of-bounds ranges, but when I checked both the maximum of the end coordinates in the bed and the max in the bigwig, all ranges were in-bounds.

Any suggestions would be appreciated.

[vivekbhr]

Hi Can you post the command the you are using, and the output error, but this time using only single processor (-p 1) ? This will give more idea about the error.

[ATpoint]

I used

 computeMatrix reference-point -R ~/input.bed -S ../input.bigwig --outFileName out.gzmatrix --outFileNameMatrix ouzt.tab -a 2000 -b 2000 -bs 25 --missingDataAsZero --referencePoint center -p 1

[vivekbhr]

How does the traceback look this time?

[kristian.lichtenberg]

I get the same problem:

computeMatrix reference-point -S myfile.bw -R mysummit.summit --referencePoint center -b=3000 -a=3000 -out output.matrix.gz -p 1

Traceback (most recent call last): File "/usr/local/bin/computeMatrix", line 7, in <module> main() File "/usr/local/lib/python2.7/site-packages/deeptools/computeMatrix.py", line 378, in main hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args) File "/usr/local/lib/python2.7/site-packages/deeptools/heatmapper.py", line 247, in computeMatrix keepExons=keepExons) File "/usr/local/lib/python2.7/site-packages/deeptools/mapReduce.py", line 144, in mapReduce res = list(map(func, TASKS)) File "/usr/local/lib/python2.7/site-packages/deeptools/heatmapper.py", line 173, in compute_sub_matrix_wrapper return heatmapper.compute_sub_matrix_worker(*args) File "/usr/local/lib/python2.7/site-packages/deeptools/heatmapper.py", line 454, in compute_sub_matrix_worker upstream.insert(0, (upstream[0][0] - padLeft, upstream[0][0])) IndexError: list index out of range

*I see now that a the last three errors are slightly different (?).

** what I could find online was suggestions to update Numpy, but I recently installed Deeptools on this machine and it is already up to date:

 pip install -U deeptools

Requirement already up-to-date: deeptools in /usr/local/lib/python2.7/site-packages Requirement already up-to-date: numpy>=1.9.0 in /usr/local/lib/python2.7/site-packages (from deeptools) Requirement already up-to-date: matplotlib>=1.4.0 in /usr/local/lib/python2.7/site-packages (from deeptools) Requirement already up-to-date: pysam>=0.8.2 in /usr/local/lib/python2.7/site-packages (from deeptools) Requirement already up-to-date: numpydoc>=0.5 in /usr/local/lib/python2.7/site-packages (from deeptools) Requirement already up-to-date: pyBigWig>=0.2.1 in /usr/local/lib/python2.7/site-packages (from deeptools) Requirement already up-to-date: scipy>=0.17.0 in /usr/local/lib/python2.7/site-packages (from deeptools) Requirement already up-to-date: twobitreader>=3.1.4 in /usr/local/lib/python2.7/site-packages (from deeptools) Requirement already up-to-date: pyparsing!=2.0.0,!=2.0.4,!=2.1.2,>=1.5.6 in /usr/local/lib/python2.7/site-packages (from matplotlib>=1.4.0->deeptools) Requirement already up-to-date: python-dateutil in /usr/local/lib/python2.7/site-packages (from matplotlib>=1.4.0->deeptools) Requirement already up-to-date: cycler in /usr/local/lib/python2.7/site-packages (from matplotlib>=1.4.0->deeptools) Requirement already up-to-date: pytz in /usr/local/lib/python2.7/site-packages (from matplotlib>=1.4.0->deeptools) Requirement already up-to-date: six>=1.5 in /usr/local/lib/python2.7/site-packages (from python-dateutil->matplotlib>=1.4.0->deeptools)

[vivekbhr]

Numpy issue is possible, but could also be an issue with your summits file.. What happens if you try any other bed file instead of mysummit.summit ?

[kristian.lichtenberg]

Thanks for the reply! I get the same problem.

I run the exact same code on my laptop which had installed deeptools and dependencies back in June and it works.

[vivekbhr]

What's your deeptools version? What happens if you try this with the latest version or develop version of deeptools? If the same command worked with same files before, but not now, them it much be the problem with one of the dependencies. Best is to install deeptools within the conda environment (check the docs), sometimes older versions of dependencies are still installed with new version and they conflict with each other.

If it still doesn't fix the issue you can share your files privately with us to help pinpoint the problem.

[aebmad]

I'm having the exact same issue using the latest deeptools version from bioconda. Before trying the very latest development version of deeptools, did you find already a solution for this? Thanks!

[sankari.nam10san]

Yes the same problem for me. Older versions worked for the same files and now its not. Did anyone figure whats the problem? I am using the web version of Deeptools unfortunately that I cant change any settings much. Any kind of information would be very welcoming.

Answer 1

[aebmad]

A temporary solution is to downgrade deeptools to version 2.1.0 (I have not tried all the releases, just so happens that I was using this before I recently had to reinstall conda and all the packages). Hopefully this also gives some hints to the dev team (thanks for this great toolkit by the way!).

Answer 2

[philip.tatman]

update to deeptools 2.4.1, this bug is now fixed