msa error with cmd execution

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albizu.m • 0

@albizum-20271

Last seen 5.1 years ago

Spain

Hi, I have a R script named 'filo.R' like that:

    suppressMessages(library(msa))
    filepath <-"C:/r/seq.txt"
    mySeqs <- readDNAStringSet(filepath)
    msa(mySeqs)

If I run this with RGui.exe there is no problem, but if I try to execute through a BAT file (windows 10) I have an error:

bat file: "C:\Program Files\R\R-3.5.2\bin\Rscript.exe" "C:\r\filo.R"

error: ERROR: Cannot open output file [internalRsequence.aln] Error in convertAlnRows(result$msa, type) : There is an invalid file! Calls: msa->msaFun->convertAlnRows Ejecución interrumpida

It seems that there is a problem writing the temporal file (in c:/r/ folder with all privileges)

software error • 1.4k views

ADD COMMENT • link 5.1 years ago albizu.m • 0

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If I use msa(mySeqs, method="ClustalOmega") instead method="ClustalW", the error does not appear.

ADD REPLY • link 5.1 years ago albizu.m • 0

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Another clue: If I double-click in BAT file run without problem, but if I run BAT file through another program fails.

ADD REPLY • link 5.0 years ago albizu.m • 0

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