I am working with one of our researchers who is doing multiple sequence alignment.
She has 200,000+ sequences in a file. Her code is basically the following:
mySeq <- readAAStringSet("myData.fa")
myFirstAlignment <- msa(mySeq)
msaPrettyPrint(MyFirstAlignment, output=c("pdf", "tex", "dvi", "asis"))
But, R is crashing during the msa function, with the following error message:
*** caught segfault ***
address 0x7f5ace31d0d0, cause 'memory not mapped'
1: .Call("RClustalW", inputSeqs, cluster, abs(gapOpening), abs(gapExtension), maxiters, substitutionMatrix, type, verbose, params, PACKAGE = "msa")
We are running R 3.4.3. I have uninstalled and reinstalled the msa package and its dependencies.
Is there anything else we could try, or is this a limitation due to the size of the data?