GATK "We encountered a non-standard non-IUPAC base in the provided reference: '13"

Question

[Phismil]

Hello Team,

I am trying to run GATK

java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R reference.fasta -I header.bam -o realigned.intervals

My reference is a trinity assembled genome with GO terms in fasta header and already indexed. I get error:

Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '13

Any idea what is going wrong?

Regards

[5heikki]

There's a non-standard non-IUPAC base in your reference.fasta? Output of:

grep -v '^>' reference.fasta | sed 's/[a,A,g,G,c,C,t,T,u,U]//g'

?

Alternatively, it could be related to the encoding of your file, in which case e.g. dos2unix could be a solution. Google knows a lot about your problem..

[Devon Ryan]

This will be due to a \r (ascii 13), so you nailed it with dos2unix.

[Phismil]

Thanks for your suggestions !