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ANGSD / angsd

Program for analysing NGS data.
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problems with estAvgError.R #613

Open OthmanSN opened 9 months ago

OthmanSN commented 9 months ago

Hi All,

I am using ANGSD to perform multipop ABBA-BABA test.

I was able to run -doAbbababa2 but have issues when I run estAvgError.R R script.

I get the following error

"Error in seq.default(1, lenList, numComb) : wrong sign in 'by' argument Calls: seq -> seq.default Execution halted"

I am not sure how to resolve this issue.

Thank you very much for your help. Regards SITI

EwersAquaGenomics commented 8 months ago

I also receive errors when trying to run estAvgError.R. These error messages differ whether I run the following command on a computing cluster or locally: Rscript DSTAT angsdFile="bam.ABBABABA" out="result" sizeFile=”sizeFile.size” nameFile=”popNames.name”

When I try to run the following command on the computing cluster, I get:

-bash: /data100/software/ANGSD/v0.929/bin/angsd/R/: Not a directory

When I try to run the same command locally on my laptop, I get the following error:

(base) xx@ff ABBABABA % Rscript DSTAT angsdFile="bam.ABBABABA" out="result" sizeFile=”sizeFile.size” nameFile=”popNames.name”

angsdFile: bam.ABBABABA errFile: FALSE nameFile: ”popNames.name” sizeFile: ”sizeFile.size” out: result addErr: FALSE nIter: 100 maxErr: 0.02

Fehler in file(file, "rt") : kann Verbindung nicht öffnen Ruft auf: unlist -> read.table -> file Ausführung angehalten

Any ideas? Thank you in advance, Christine