bwa read group tagging failed in PBS cluster

Question

[chenyangkang24]

Hi guys,

I was trying to build a PBS script for bwa alignment (reads mapping) and submit it to the PBS cluster, but failed with this: [E::bwa_set_rg] no ID within the read group line

my code:

bwa mem -t 20 -R '@RG\tID:NL\tSM:NL\tLB:NL\tPL:Illumina' reference.fasta 1.fastq.clean.gz 2.fastq.clean.gz > NL.0.sam

and I have tried this:

bwa mem -t 20 -R @RG\tID:NL\tSM:NL\tLB:NL\tPL:Illumina reference.fasta 1.fastq.clean.gz 2.fastq.clean.gz > NL.0.sam

or this: '\@RG\tID:NL\tSM:NL\tLB:NL\tPL:Illumina'

All above in the PBS script, which starts like " #PBS -N call "...

But when I type the command in linux shell command line directly, everything goes fine.

Can anyone gives me some clues?

[Ram]

Wild suggestion: Can you try $'@RG\tID:NL\tSM:NL\tLB:NL\tPL:Illumina' (just adds a $ before the single quoted string)? If that works, there is a communication gap on the \t character between the shell and bwa.