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parklab / HiNT

HiC for copy Number variation and Translocation detection
MIT License
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hint cnv -f juicer: TypeError: 'int' object is not subscriptable #2

Open sidiropoulos opened 4 years ago

sidiropoulos commented 4 years ago

Hi,

I'm experiencing the following error when I'm running hint cnv using a juicer .hic file as input, both with my own and the test dataset.

$ hint cnv -f juicer -m test.hic --refdir hg19 --bicseq /home/projects/cu_10027/apps/software/BICseq2-seg_v0.7.3 -e MboI -r 50000 -g hg19 -o ./ -n test -p 12
[15:32:05] Argument List:
[15:32:05] Hi-C contact matrix = test.hic
[15:32:05] Hi-C contact matrix format = juicer
[15:32:05] resolution = 50000 kb
[15:32:05] Genome = hg19
[15:32:05] BICseq directory = /home/projects/cu_10027/apps/software/BICseq2-seg_v0.7.3
[15:32:05] Name = test
[15:32:05] Output directory = ./
HiC version:  8
Error finding block data

Traceback (most recent call last):
  File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/bin/hint", line 201, in <module>
    main()
  File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/bin/hint", line 194, in main
    cnvrun(argparser)
  File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/lib/python3.6/site-packages/HiNT/runhint.py", line 79, in cnvrun
    rowSumFilesInfo = getGenomeRowSums(opts.resolution, opts.matrixfile, chromlf, opts.outdir,opts.name)
  File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/lib/python3.6/site-packages/HiNT/getGenomeRowSumsFromHiC.py", line 69, in getGenomeRowSums
    sumInfo = getSumPerChrom(i, j, hicfile, binsize, chroms, chromInfo, sumInfo)
  File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/lib/python3.6/site-packages/HiNT/getGenomeRowSumsFromHiC.py", line 20, in getSumPerChrom
    result = straw('NONE', hicfile, str(chr1), str(chr2), 'BP', binsize)
  File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/lib/python3.6/site-packages/HiNT/straw.py", line 543, in straw
    blockBinCount=list1[0]
TypeError: 'int' object is not subscriptable

I installed Hint using miniconda3/4.5.4 and python=3.6 Is there any known workaround?

Thanks, Nikos

suwangbio commented 4 years ago

Hi Nikos,

(1) Please make sure that the reference directory is the current directory that you run this job, since your input for —refdir is hg19, which equals to ./hg19. (2) For the resolution, I guess you want to use 50kb, so your input should be 50 but not 50000, the unit is kb in HiNT-cnv. Please refer to our instructions on github. I think this is the reason that caused the error in your case.

Thanks, Su

On Nov 11, 2019, at 09:38, Nikos Sidiropoulos notifications@github.com wrote:

Hi,

I'm experiencing the following error when I'm running hint cnv using a juicer .hic file as input, both with my own and the test dataset.

$ hint cnv -f juicer -m test.hic --refdir hg19 --bicseq /home/projects/cu_10027/apps/software/BICseq2-seg_v0.7.3 -e MboI -r 50000 -g hg19 -o ./ -n test -p 12 [15:32:05] Argument List: [15:32:05] Hi-C contact matrix = test.hic [15:32:05] Hi-C contact matrix format = juicer [15:32:05] resolution = 50000 kb [15:32:05] Genome = hg19 [15:32:05] BICseq directory = /home/projects/cu_10027/apps/software/BICseq2-seg_v0.7.3 [15:32:05] Name = test [15:32:05] Output directory = ./ HiC version: 8 Error finding block data

Traceback (most recent call last): File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/bin/hint", line 201, in main() File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/bin/hint", line 194, in main cnvrun(argparser) File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/lib/python3.6/site-packages/HiNT/runhint.py", line 79, in cnvrun rowSumFilesInfo = getGenomeRowSums(opts.resolution, opts.matrixfile, chromlf, opts.outdir,opts.name) File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/lib/python3.6/site-packages/HiNT/getGenomeRowSumsFromHiC.py", line 69, in getGenomeRowSums sumInfo = getSumPerChrom(i, j, hicfile, binsize, chroms, chromInfo, sumInfo) File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/lib/python3.6/site-packages/HiNT/getGenomeRowSumsFromHiC.py", line 20, in getSumPerChrom result = straw('NONE', hicfile, str(chr1), str(chr2), 'BP', binsize) File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/lib/python3.6/site-packages/HiNT/straw.py", line 543, in straw blockBinCount=list1[0] TypeError: 'int' object is not subscriptable I installed Hint using miniconda3/4.5.4 and python=3.6 Is there any known workaround?

Thanks, Nikos

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sidiropoulos commented 4 years ago

Hi Su,

Changing the resolution to 50 did the trick. Thanks for the quick response and for a great tool!

Best, Nikos