svtools copynumber error *** Break *** segmentation violation

[cusanchang]

Hello,

I installed svtools, cnvnator, root, lumpy-sv by using "mamba install -c conda-forge -c bioconda root cnvnator lumpy-sv svtools", the installation is smoothly. When I run "svtools copynumber --cnvnator cnvnator -s C005 -w 1000 -r ../1.ALL_samples_output/C005.root -c coordinates -i gt/C005.vcf -o cn/C005.vcf", it show error as below. The Root version is ROOT 6.22, I also tried ROOT 6.12, there is still the error. Could anyone can help on this?

Thanks!

*** Break *** segmentation violation

===========================================================
There was a crash.
This is the entire stack trace of all threads:

#0 0x00007fd74f73446c in waitpid () from /lib64/libc.so.6
#1 0x00007fd74f6b1f62 in do_system () from /lib64/libc.so.6
#2 0x00007fd7511d03c4 in TUnixSystem::StackTrace() () from /home/suhuachang/miniconda3/envs/cnvnator/bin/../lib/libCore.so.6.20
#3 0x00007fd7511d3017 in TUnixSystem::DispatchSignals(ESignals) () from /home/suhuachang/miniconda3/envs/cnvnator/bin/../lib/libCore.so.6.20
#4
#5 0x0000559d2da14f62 in Genotyper::getReadCount(int, int) ()
#6 0x0000559d2da162a5 in Genotyper::printGenotype(std::__cxx11::basic_string<char, std::char_traits, std::allocator >, int, int, bool, bool) ()
#7 0x0000559d2d9e93f7 in HisMaker::genotype(std::__cxx11::basic_string<char, std::char_traits, std::allocator >*, int, bool, bool) ()
#8 0x0000559d2d9aefc9 in main ()

The lines below might hint at the cause of the crash.
You may get help by asking at the ROOT forum http://root.cern.ch/forum
Only if you are really convinced it is a bug in ROOT then please submit a
report at http://root.cern.ch/bugs Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.

#5 0x0000559d2da14f62 in Genotyper::getReadCount(int, int) ()
#6 0x0000559d2da162a5 in Genotyper::printGenotype(std::__cxx11::basic_string<char, std::char_traits, std::allocator >, int, int, bool, bool) ()
#7 0x0000559d2d9e93f7 in HisMaker::genotype(std::__cxx11::basic_string<char, std::char_traits, std::allocator >*, int, bool, bool) ()
#8 0x0000559d2d9aefc9 in main ()

Traceback (most recent call last):
File "/home/suhuachang/miniconda3/envs/cnvnator/bin/svtools", line 11, in
sys.exit(main())
File "/home/suhuachang/miniconda3/envs/cnvnator/lib/python2.7/site-packages/svtools/cli.py", line 79, in main
sys.exit(args.entry_point(args))
File "/home/suhuachang/miniconda3/envs/cnvnator/lib/python2.7/site-packages/svtools/copynumber.py", line 114, in run_from_args
sv_readdepth(stream, args.sample, args.root, args.window, args.output, args.cnvnator, args.coordinates)
File "/home/suhuachang/miniconda3/envs/cnvnator/lib/python2.7/site-packages/svtools/copynumber.py", line 26, in sv_readdepth
write_copynumber(vcf_file, sample, vcf_out, cn)
File "/home/suhuachang/miniconda3/envs/cnvnator/lib/python2.7/site-packages/svtools/copynumber.py", line 78, in write_copynumber
update_line_copynumber(v, cn_list, i)
File "/home/suhuachang/miniconda3/envs/cnvnator/lib/python2.7/site-packages/svtools/copynumber.py", line 34, in update_line_copynumber
v[9] = v[9] + ':' + str(cn_list[i])
IndexError: list index out of range