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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
396 stars 38 forks source link

Segmentation fault (core dumped) while generaing a genome graph #81

Open lingliao opened 1 year ago

lingliao commented 1 year ago

I attached the output while trying to generate a genome graph... Any suggestion would be appreciated! [M::main::0.0014.79] loaded the graph from "bap1_hg38.fa" [M::mg_index::0.0041.46] indexed the graph [M::mg_opt_update::0.0041.46] occ_max1=10; lc_max_occ=2 [M::ggen_map::0.0051.40] loaded file "bap1_CHM13v2.0.fa" [M::ggen_map::0.005*1.40] mapped 1 sequence(s) to the graph Segmentation fault (core dumped)

lh3 commented 1 year ago

Could you share the input sequences? Thanks.

lingliao commented 1 year ago

Thanks for the reply!! I also tried the test files, MT-chimp.fa and MT-human.fa, they also only work when t = 1, minigraph -cxggs -t 1 MT-chimp.fa MT-human.fa > graph_test.gfa My data also only works when t = 1. Would you please let me know why it couldn't work with more thread?

lh3 commented 1 year ago

It works on my machine. Maybe something specific to your machine.

lingliao commented 1 year ago

I see, that would be weird, we are using in-campus storage1, and sorry I didn't share the data here, I don't have access to download file...