Hey :)

I am trying to do a bisulfite alignment with qAlign function. This is my command:

align <- qAlign("/analysis/SampleFile.txt","/analysis/refgenome.fa",aligner="Rbowtie",bisulfite="dir",alignmentParameter=" -m 3 -v 5 --best --strata")

I always get the following error whenever i try to pass alignment parameters no matter what the parameters are:

Error in checkForRemoteErrors(val) :
  one node produced an error: Error on server.whorke.de processing sample /testread.fasta : bowtie (CtoT) failed to perform the alignments.

Any suggestion?

Thanks in advance!

Best,

Amer