lh3 / minigraph

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

An error occurred when the sample.gfa file was generated #116

Closed jiangwenhao3001 closed 2 weeks ago

jiangwenhao3001 commented 2 weeks ago

``When run the following command line minigraph -xggs -t16 13C.fa MP.fa > MP.gfa The following error occurs [M::main::1.1060.52] loaded the graph from "13C.fa" [M::mg_index::9.5171.53] indexed the graph [M::mg_opt_update::10.0511.50] occ_weight=20, occ_max1=154; 95 percentile: 2 [M::ggen_map::11.5351.39] loaded file "MP.fa" [W::worker_for] stable sequence "chr10" already present in the graph. This will lead to inconsi stent rGFA. [W::worker_for] stable sequence "chr11" already present in the graph. This will lead to inconsi stent rGFA. [W::worker_for] stable sequence "chr12" already present in the graph. This will lead to inconsi stent rGFA. [M::ggen_map::75.104*8.40] mapped 12 sequence(s) to the graph [W] stable sequence 'chr10' associated with different ranks on segment 's9208': 0 != 1 [W] stable sequence 'chr10' associated with different ranks on segment 's9209': 0 != 1 [W] stable sequence 'chr10' associated with different ranks on segment 's9210': 0 != 1 [W] stable sequence 'chr10' associated with different ranks on segment 's9211': 0 != 1

How to resolve the above error

lh3 commented 2 weeks ago

You need to give each sequence a distinct name.