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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Error running test example #1158

Open aziesel opened 1 year ago

aziesel commented 1 year ago

Hello,

I've installed Cactus from the pre-compiled binary on an Azure VM running Ubuntu 20.04. I'm unable to get the example "cactus ./js ./examples/evolverMammals.txt ./evolverMammals.hal" to run successfully. Attached is my complete error log from that run.

Any insight you might be able to provide regarding this error is greatly appreciated, thank you in advance.

error.log

aziesel commented 1 year ago

As a follow-up, I tried to run the example using the step-by-step instructions generated by "cactus-prepare examples/evolverMammals.txt --outDir steps-output --outSeqFile steps-output/evovlerMammals.txt --outHal steps-output/evolverMammals.hal --jobStore jobstore".

This did work, on the same install that generated the above described error. I'm not certain as to what the difference is between running cactus and individually running the steps indicated by cactus-prepare.

glennhickey commented 1 year ago

Seems like maybe an installation / environment problem. Your log has lastz failing with 

 stderr=Can't understand "--format=paf:minimap2"

which shouldn't happen if you're using the lastz included in cactus...

aziesel commented 1 year ago

Thank you for this suggestion, it worked and I can now run the single command from the example successfully. I'm still not sure why cactus and the steps outlined by cactus-prepare behaved differently with another install of LASTZ in my PATH, though, but going forward I have a solution. Thanks!