search

hall-lab / svtools

Tools for processing and analyzing structural variants.
MIT License
147 stars 54 forks source link

ValueError: max() arg is an empty sequence #325

Open Hubuyan opened 1 year ago

Hubuyan commented 1 year ago

Hi Dave,

I try to genotype around 1.7k samples with svtools. lsort worked but, I can not do lmerge step.

I keep having this following error:

Traceback (most recent call last): File "/home/zhiyan/.conda/envs/AGAT/bin/svtools", line 10, in sys.exit(main()) File "/home/zhiyan/.conda/envs/AGAT/lib/python2.7/site-packages/svtools/cli.py", line 79, in main sys.exit(args.entry_point(args)) File "/home/zhiyan/.conda/envs/AGAT/lib/python2.7/site-packages/svtools/lmerge.py", line 638, in run_from_args weighting_scheme=args.weighting_scheme) File "/home/zhiyan/.conda/envs/AGAT/lib/python2.7/site-packages/svtools/lmerge.py", line 601, in l_cluster_by_line v_id = r_cluster(BP_l, sample_order, v_id, use_product, vcf, vcf_out, include_genotypes, weighting_scheme) File "/home/zhiyan/.conda/envs/AGAT/lib/python2.7/site-packages/svtools/lmerge.py", line 532, in r_cluster v_id = merge(BP_r, sample_order, v_id, use_product, vcf, vcf_out, include_genotypes, weighting_scheme) File "/home/zhiyan/.conda/envs/AGAT/lib/python2.7/site-packages/svtools/lmerge.py", line 507, in merge var=create_merged_variant(BP, cliq, v_id, vcf, use_product, weighting_scheme) File "/home/zhiyan/.conda/envs/AGAT/lib/python2.7/site-packages/svtools/lmerge.py", line 242, in create_merged_variant max_i_R = p_R.index(max(p_R)) ValueError: max() arg is an empty sequence

I have run several individual without any issues，but there were issues with these 1.7k samples.

If you can give me any idea to solve this problem, it would be awesome.

Best, Jason Hoo