correct_links: Aborted

[guo-cheng]

Hi, I am running SALSA on a GFA created by Hifiasm, but it crashed.

My command line: ~/miniconda3/envs/py2.7/bin/python /public1/home/ligch/software/SALSA/run_pipeline.py -a /public1/home/ligch/Harm_Hass_genome/Harm/03_HiC_assembly/reference/Harm.primary.asm.p_ctg.fa -l /public1/home/ligch/Harm_Hass_genome/Harm/03_HiC_assembly/reference/Harm.primary.asm.p_ctg.fa.fai -b Harm.primary.alignment.sorted.bed -e GATC -o Harm.primary.scaffold -m yes -p yes -g /public1/home/ligch/Harm_Hass_genome/Harm/03_HiC_assembly/reference/Harm.primary.asm.p_ctg.gfa

The Log file: bedfile loaded Starting Iteration 1 bedfile started bedfile loaded Done loading GFA file Number of Nodes = 116 Number of Edges = 40 correct_links: /usr/include/boost/graph/two_bit_color_map.hpp:86: void boost::put(const boost::two_bit_color_map<IndexMap>&, typename boost::property_traits<PMap>::key_type, boost::two_bit_color_type) [with IndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_name_t, std::basic_string >, long unsigned int>; typename boost::property_traits<PMap>::key_type = long unsigned int]: Assertion `(std::size_t)i < pm.n' failed. /bin/sh: line 1: 66103 Aborted (core dumped) /public1/home/ligch/software/SALSA/correct_links -g /public1/home/ligch/Harm_Hass_genome/Harm/03_HiC_assembly/reference/Harm.primary.asm.p_ctg.gfa -l Harm.primary.scaffold/contig_links_scaled_sorted_iteration_1 > Harm.primary.scaffold/tmp.links

[skoren]

We've never tested with the gfa from hifiasm so it may be some incompatibility. In general, the contig gfa isn't that useful for scaffolding information since most connectivity is removed so I wouldn't bother including it, I doubt it would make any difference.