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?
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chenyangkang24 •
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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\tcharacter between the shell and bwa.