About RuntimeError: Invalid interval bounds!
Yung-Chih Lai
Hi,
I have a MeDIP-Seq bigwig file and a human hg19 CpG islands bed file. The bed file was downloaded from the UCSC Table Browser. When I run computeMatrix only with upstream 1,000 bp, it did well (fig1 & Terminal.txt) and I can get its profile (i.e. T8E_HMC.png). However, it was failed and showed “RuntimeError: Invalid interval bounds!” when I run computeMatrix with both upstream and downstream 1,000 bp (fig1 & Terminal.txt). I checked the Problematic region: chr6_mcf_hap5:4834395-4831853, and found that there is missing data (fig2). Could you help me to deal with this issue? Thanks a lot.
Best,
Gary
Devon Ryan
Thanks for reporting this issue. We've run into this ourselves and
think we've fixed it already for the next release. Once that one is
available (we'll send an email out to the list), you should be able to
just upgrade and have this work.
Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany
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Yung-Chih Lai
Yung-Chih Lai
Hi Devon,
I have upgraded the deepTools, but it still occurs the error of Invalid interval bounds below. This time, I would like to see whether DNA methylation is enriched on CpG Islands. The data I have are: (1) T8E_MC.bigwig: a MeDIP-Seq bigwig file produced by bamcompare, and (2) hg19_CpGIslands.bed: an hg19 CpG Islands bed file downloaded from UCSC Table Browser. Could you help me again? Thanks a lot.
Best,
Gary
T8E_MC.bigwig
http://68.181.92.180/~Gary/temporal/T8E_MC.bigwig
hg19_CpGIslands.bed
http://68.181.92.180/~Gary/temporal/hg19_CpGIslands.bed
gary > uname -a
Darwin dynamic2-095-196.hsc.usc.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
gary > computeMatrix --version
computeMatrix 2.0.1
gary > computeMatrix scale-regions --regionsFileName hg19_CpGIslands.bed --scoreFileName T8E_MC.bigwig --upstream 1000 --downstream 1000 --regionBodyLength 1000 --binSize 1 --sortRegions no --sortUsing mean --averageTypeBins mean --numberOfProcessors 6 --outFileName CpGIland_T8E_MC.gz
Found:
intervals: 28691
no groups found
Exception found. Message: Invalid interval bounds!
Problematic region: chr6_mcf_hap5:4834395-4831853
Traceback (most recent call last):
File "/Users/gary/anaconda/bin/computeMatrix", line 7, in <module>
main()
File "/Users/gary/anaconda/lib/python2.7/site-packages/deeptools/computeMatrix.py", line 366, in main
hm.computeMatrix(scores_file_list, bed_file, parameters, verbose=args.verbose)
File "/Users/gary/anaconda/lib/python2.7/site-packages/deeptools/heatmapper.py", line 71, in computeMatrix
mp_args).get(9999999)
File "/Users/gary/anaconda/lib/python2.7/multiprocessing/pool.py", line 567, in get
raise self._value
RuntimeError: Invalid interval bounds!
Fidel Ramirez
Fidel Ramirez
Friederike Dündar
Yung-Chih Lai
Hi Fidel,
Many thanks for your information. Please see the error message I re-run with --numberOfProcessors 1 below. The region (i.e. chr6_mcf_hap5:4834395-4831853) show in the error message is at the end of an unplaced chromosome (fig1). However, the region (i.e. chr6_mcf_hap5:4834395-4831853) is not a CpG island in my hg19_CpGIslands.bed file (fig2), then I cannot remove it in my bed file. The bigwig file was produced by an early version (not 2.0.1) of bamcompare. Is it an issue? I really appreciate your help.
Best,
Gary
hg19_CpGIslands.bed
http://68.181.92.180/~Gary/temporal/hg19_CpGIslands.bed
gary > uname -a
Darwin dynamic2-095-196.hsc.usc.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
gary > computeMatrix --version
computeMatrix 2.0.1
gary > ls
2913peak_T8E_HMC.gz T8L_HMC_enhancer.bed
2913peak_T8L_HMC.gz T8L_MC.bed
2913peak_T9E_HMC.gz T8L_MC.bigwig
2913peak_T9L_HMC.gz T9E_HMC.bigwig
MeDIP_T8L_INPUT_NonRPKM.bigwig T9E_HMC_enhancer.bed
T8E_HMC.bigwig T9E_MC.bed
T8E_HMC_enhancer.bed T9E_MC.bigwig
T8E_HMC_enhancer_vertebrate.gz T9L_HMC.bigwig
T8E_MC.bed T9L_HMC_enhancer.bed
T8E_MC.bigwig T9L_MC.bed
T8EandT9E_2913peak T9L_MC.bigwig
T8EandT9E_2913peak.bed hg19_CpGIslands.bed
T8EandT9E_5mC_CpGIsland result/
T8L_HMC.bigwig
gary > computeMatrix scale-regions --regionsFileName hg19_CpGIslands.bed --scoreFileName T8E_MC.bigwig --upstream 1000 --downstream 1000 --regionBodyLength 1000 --binSize 1 --sortRegions no --sortUsing mean --averageTypeBins mean --numberOfProcessors 1 --outFileName CpGIland_T8E_MC.gz
Found:
intervals: 28691
no groups found
Exception found. Message: Invalid interval bounds!
Problematic region: chr6_mcf_hap5:4834395-4831853
Traceback (most recent call last):
File "/Users/gary/anaconda/bin/computeMatrix", line 7, in <module>
main()
File "/Users/gary/anaconda/lib/python2.7/site-packages/deeptools/computeMatrix.py", line 366, in main
hm.computeMatrix(scores_file_list, bed_file, parameters, verbose=args.verbose)
File "/Users/gary/anaconda/lib/python2.7/site-packages/deeptools/heatmapper.py", line 73, in computeMatrix
res = map(compute_sub_matrix_wrapper, mp_args)
File "/Users/gary/anaconda/lib/python2.7/site-packages/deeptools/heatmapper.py", line 16, in compute_sub_matrix_wrapper
return heatmapper.compute_sub_matrix_worker(*args)
File "/Users/gary/anaconda/lib/python2.7/site-packages/deeptools/heatmapper.py", line 286, in compute_sub_matrix_worker
parameters['verbose'])
File "/Users/gary/anaconda/lib/python2.7/site-packages/deeptools/heatmapper.py", line 504, in coverage_from_big_wig
zones[-1][1])
RuntimeError: Invalid interval bounds!
gary >
Fidel Ramirez
Fidel Ramirez