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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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cactus-graph map : filter-paf-deletions unrecognized option -s #970

Closed IsaacDiaz026 closed 1 year ago

IsaacDiaz026 commented 1 year ago

Hello,

I am trying to run cactus-graphmap using the following command.

cactus-graphmap jobstore test_seqfile.txt test_run.gfa test_run.paf --workDir /bigdata/seymourlab/idiaz026/Citrus_non-coding_evolution/2023-03-15_pangenome_assembly/workdir --reference PUMM --binariesMode local --mapCores 1 --outputFasta test_run.gfa

RuntimeError: Command ['filter-paf-deletions', '/bigdata/seymourlab/idiaz026/Citrus_non-coding_evolution/2023-03-15_pangenome_assembly/workdir/4bf95a89eb595edf8d1a962983d7813f/3478/84a3/tmpdufz9v4y/mg.gfa.vg', '/bigdata/seymourlab/idiaz026/Citrus_non-coding_evolution/2023-03-15_pangenome_assembly/workdir/4bf95a89eb595edf8d1a962983d7813f/3478/84a3/tmpdufz9v4y/mg.gfa.trans', '/bigdata/seymourlab/idiaz026/Citrus_non-coding_evolution/2023-03-15_pangenome_assembly/workdir/4bf95a89eb595edf8d1a962983d7813f/3478/84a3/tmpdufz9v4y/mg.paf', '-d', '10000000', '-v', '-p', '-t', '1', '-m', '0.01', '-s', '2.0'] exited 1: stdout=, stderr=filter-paf-deletions: invalid option -- 's'

I am unsure if this a version issue. Any thoughts?

glennhickey commented 1 year ago

Definitely looks like a version issue. The filter-paf-deletions that comes with cactus definitely has a -s option. You may want to try re-installing and/or making sure your PATH is pointing to the correct place for the cactus binaries.