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hall-lab / svtools

Tools for processing and analyzing structural variants.
MIT License
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Svtools copynumber error #287

Open deepalivasoya opened 5 years ago

deepalivasoya commented 5 years ago

Hello,

I am running svtools to add the copynumber information in vcf. CNVnator is up running and I have created hist root file. Genotyping is also done successfully. In the next step where we add copynumner in genotype, I am having the following issue:

/software/deepali/CNVnator/cnvnator: error while loading shared libraries: libCore.so: wrong ELF class: ELFCLASS32 Traceback (most recent call last): File "/software/deepali/anaconda/envs/svtools/bin/svtools", line 11, in sys.exit(main()) File "/software/deepali/anaconda/envs/svtools/lib/python2.7/site-packages/svtools/cli.py", line 78, in main sys.exit(args.entry_point(args)) File "/software/deepali/anaconda/envs/svtools/lib/python2.7/site-packages/svtools/copynumber.py", line 107, in run_from_args sv_readdepth(stream, args.sample, args.root, args.window, args.output, args.cnvnator, args.coordinates) File "/software/deepali/anaconda/envs/svtools/lib/python2.7/site-packages/svtools/copynumber.py", line 26, in sv_readdepth write_copynumber(vcf_file, sample, vcf_out, cn) File "/software/deepali/anaconda/envs/svtools/lib/python2.7/site-packages/svtools/copynumber.py", line 77, in write_copynumber update_line_copynumber(v, cn_list, i) File "/software/deepali/anaconda/envs/svtools/lib/python2.7/site-packages/svtools/copynumber.py", line 32, in update_line_copynumber if cn_list[i] == -1: IndexError: list index out of range cat: write error: Broken pipe

I have root/5.34.23 installed on server. I dont understand the compiling error while both svtools and cnvnator are working fine on its own. It would be great if I get some help asap here.

Cheers, Deepali

ashwinichhipa commented 4 years ago

Hi Deepali, I also came across this issue, and updating ROOT to the latest version solved it for me.

Thanks!