MetaTrans R-3.4.4

[Roberto Villegas-Diaz]

Hello,

I've been trying to execute the Pipeline on Ubuntu (after giving up of CentOS), but I keep getting an error message when executing the DESeq2.R script. I'm using R-3.4.4 I saw previous comments on this forum and added to this script the line colnames(CountTable) <- NULL however after this on the following line: 

ddsMF <- DESeqDataSetFromMatrix(countData = CountTable,
                                colData = CountData,
                                design =  as.formula(paste("~",paste(listoffactors,collapse="+"))))

The program halts and returns the following error message:
Error in if (all(var == var[1])) { :
  missing value where TRUE/FALSE needed
Calls: DESeqDataSetFromMatrix -> DESeqDataSet
Execution halted

Any ideas what could it be? I've been trying to tweak the DESeq.R myself without success.

Kind regards,
Roberto Villegas-Diaz

PS: The command I'm executing is
./metatrans -nqc -nrrnarem -m5nr -nfunmap

Because I didn't get any error during the mapping phase.

[bth...@gmail.com]

Hello, I've just found my error, it was a name tag used on the metadata.txt (NA) which was causing some conflicts with the R interpreter. Thanks.

[metatr...@gmail.com]

Hi Roberto,

Glad to know you found the cause of the error. As mentioned in a previous post we are not able right
now to test and find bugs in other environments. So far, our recommendation to use MetaTrans is to
use a similar environment in which it was created.

Sorry for the inconvenience this may cause

Greetings