linearham run_bootstrap_asr_ess.R

[Evi Van Itallie]

hello, 
I have a question about linearham. We are trying to use it in a container. Everything goes great, and then when the "run_bootstrap_asr_ess.R" script runs we get the same error no matter what we do. It looks like a problem with the R parallelization. Potentially, with how this is interacts with nodes on our cluster. I know this is a bit of a shot in the dark, but do you have any thoughts on how to fix this? Thank you!
Elizabeth / Evi 

 The last lines of the output file are:

Rscript --slave --vanilla scripts/run_bootstrap_asr_ess.R output/cluster-0/mcmciter20_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/lh_revbayes_run.trees output/cluster-0/cluster_seqs.fasta 0.1 0.05 1 0 output/cluster-0/mcmciter20_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/burninfrac0.1_subsampfrac0.05/linearham_run.trees output/cluster-0/mcmciter20_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/burninfrac0.1_subsampfrac0.05/linearham_run.log output/cluster-0/mcmciter20_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/burninfrac0.1_subsampfrac0.05/linearham_run.ess

scons: building terminated because of errors.

There error is:

Error in checkForRemoteErrors(val) : 

  2 nodes produced errors; first error: no applicable method for 'unroot' applied to an object of class "NULL"

Calls: unlist ... <Anonymous> -> dynamicClusterApply -> checkForRemoteErrors

[Duncan Ralph]

I've never run that stuff in parallel, but our best guess is it might have to do with library export to your batch nodes: https://github.com/rspatial/terra/issues/178, so maybe loading library(ape) within the function where it seems to be crashing https://github.com/matsengrp/linearham/blob/main/scripts/run_bootstrap_asr_ess.R#L51

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