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matsengrp / linearham

A Bayesian Phylo-HMM for B cell receptor sequence analysis
http://matsengrp.github.io/linearham
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Alignment Fail #97

Open colejensen opened 1 month ago

colejensen commented 1 month ago

Hello,

I'm trying to use linearham. I'm testing it out with some simulated data (made with BCR-Phylo) but the alignment step seems to be failing.

I run the following lines of code

scons --run-partis --fasta-path= --locus={igh|igk|igl} --outdir=

--parameter-dir=

scons --run-linearham --outdir=

--partis-yaml-file= --parameter-dir=

But I get 'Error 1' which then points to the alignment step. I am using the docker container and mounting a folder that contains the fasta file(s) used. I've also attached some of the files used to run these steps. Any help would be appreciated. testing_data.zip

psathyrella commented 1 month ago

I'm not sure what that could be offhand. Could you post the full std out and stack trace?

colejensen commented 1 month ago

Sure, these are the outputs I get. outputs.zip

psathyrella commented 1 month ago

I don't see a stack trace in the zip anywhere, am I missing it? So I'm still not sure what "Error 1" refers to. In this log file, though, ./cluster-0/mcmciter10000_mcmcthin10_tuneiter5000_tunethin100_numrates4_rngseed0/revbayes_run.stdout.log it seems like it can't find the input fasta file for cluster 0, so perhaps whichever step is making that file is having issues. I also note that the partis_run.stdout.log file also says that it only processed one cluster, whereas you have subdirs for two clusters, so perhaps that is the issue. No idea if this is the issue, but if your clusters are very small, you may need to increase them since it by default discards very small clusters.