search

ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
Other
520 stars 111 forks source link

Cactus graph map split fails on rgfa-split step #1145

Closed IsaacDiaz026 closed 1 year ago

IsaacDiaz026 commented 1 year ago

I am trying to use graph map-split with the following command

cactus-graphmap-split jobstore test_seqfile.txt first_run.gfa first_run.paf --workDir /bigdata/seymourlab/idiaz026/Citrus_non-coding_evolution/2023-03-15_pangenome_assembly/workdir --outDir /bigdata/seymourlab/idiaz026/Citrus_non-coding_evolution/2023-03-15_pangenome_assembly/workdir --reference PWN --binariesMode local --cleanWorkDir onSuccess

and receive an error on the rgfa-split step

RuntimeError: Command ['rgfa-split', '-p', '/bigdata/seymourlab/idiaz026/Citrus_non-coding_evolution/2023-03-15_pangenome_assembly/workdir/fc47df20b80d5e509bee86a2939e1e56/8320/c791/tmpy2q5q3in/mg.paf', '-b', '/bigdata/seymourlab/idiaz026/Citrus_non-coding_evolution/2023-03-15_pangenome_assembly/workdir/fc47df20b80d5e509bee86a2939e1e56/8320/c791/tmpy2q5q3in/split_', '-Q', '2', '-a', '_AMBIGUOUS_', '-L', '/bigdata/seymourlab/idiaz026/Citrus_non-coding_evolution/2023-03-15_pangenome_assembly/workdir/fc47df20b80d5e509bee86a2939e1e56/8320/c791/tmpy2q5q3in/split.log', '-n', '0.75', '-n', '0.5', '-n', '0.25', '-T', '100000', '-T', '1000000', '-g', '/bigdata/seymourlab/idiaz026/Citrus_non-coding_evolution/2023-03-15_pangenome_assembly/workdir/fc47df20b80d5e509bee86a2939e1e56/8320/c791/tmpy2q5q3in/mg.gfa', '-G', '-r', 'id=PWN|', '-A', '5'] signaled SIGABRT: stderr=terminate called after throwing an instance of 'std::invalid_argument' what(): stol

The input paf to this command looks normal to me. All of the command arguments seem to be fine for this command.

I am using version 2.6.2

glennhickey commented 1 year ago

Where is first_run.gfa from? It must be the output of minigraph or you will get errors like this.

IsaacDiaz026 commented 1 year ago

I used the following command to get the gfa

cactus-minigraph jobstore test_seqfile.txt first_run.gfa --workDir /bigdata/seymourlab/idiaz026/Citrus_non-coding_evolution/2023-03-15_pangenome_assembly/workdir --reference PWN --binariesMode local --defaultCores 4

glennhickey commented 1 year ago

That seems about right. Are you able to try running cactus-pangenome with the latest cactus release on this data?

IsaacDiaz026 commented 1 year ago

I will try this and get back to you