hint cnv -f juicer: TypeError: 'int' object is not subscriptable

Question

hint cnv -f juicer: TypeError: 'int' object is not subscriptable

Opened this issue 5 years ago · 2 comments

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

Answer 1 · 2019-11-12T01:50:46.000Z

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 ***@***.***> 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 <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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2?email_source=notifications&email_token=AEHIZ2V3KMXRYDMWNJGWHX3QTFU4XA5CNFSM4JLWM4N2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HYN2P4Q>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEHIZ2VI44FBUTBVRCYMZHLQTFU4XANCNFSM4JLWM4NQ>.

Answer 2 · 2019-11-12T09:53:10.000Z

Hi Su,

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

Best,
Nikos