gramtools build error - Githubissues

When I run gramtools build, the software throws errors. But when I separate the variants by chromosome, the software works fine, I don't know the reason. Thanks a lot if you can help me out.

This is error:

2022-06-29 17:35:29,252 gramtools DEBUG Ran vcf_record_clustering in: 218.30659580230713 seconds 2022-06-29 17:35:29,252 gramtools INFO Running build prg from VCF(s) on /home/xxx/analyze/graph/xxx-ho/gramtools/top50/build/build.vcf [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'SVTYPE' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 2022-06-29 17:51:32,219 gramtools DEBUG Ran build prg from VCF(s) in: 1181.2732882499695 seconds 2022-06-29 17:51:32,231 gramtools INFO Running backend build 2022-06-29 17:51:32,231 gramtools DEBUG Executing command: /home/xxx/software/miniconda3/envs/gramtools/lib/python3.9/site-packages/gramtools/bin/gram build --gram_dir ./build --ref ../../refgenome.rep.fa --kmer_size 10 --max_threads 10 --all_kmers --debug 2022-06-29 17:51:32,231 gramtools DEBUG Using current working directory: /home/xxx/analyze/graph/xxx-ho/gramtools/top50 2022-06-29 17:56:27,993 gramtools ERROR Traceback: Traceback (most recent call last): File "/home/xxx/miniconda3/envs/gramtools/lib/python3.9/site-packages/gramtools/commands/report.py", line 25, in reportify original_result = f(report, action, command_paths, *args) File "/home/xxx/miniconda3/envs/gramtools/lib/python3.9/site-packages/gramtools/commands/build/build.py", line 93, in execute_gramtools_cpp_build raise Exception(f"while running backend build:\n{command_result.stderr}") Exception: while running backend build: gram: /home/brice/Desktop/main_PhD/git_repos/gramtools/libgramtools/src/prg/coverage_graph.cpp:159: marker_type cov_Graph_Builder::find_marker_type(const uint32_t&): Assertion `pos <= end_pos' failed. 2022-06-29 17:56:27,993 gramtools ERROR Unsuccessful gramtools_build. Process reported to /home/xxx/analyze/graph/xxx-ho/gramtools/top50/build/build_report.json

iqbal-lab-org / gramtools

gramtools build error #166