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Old 01-24-2012, 12:16 AM   #1
CHRYSES
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Location: Netherlands

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Unhappy Bowtie2 ( not running with option --sam-rg

Hello,

If I run bowtie2 as below, everything works fine:
bowtie2 --local -x reference.fasta -U in.fastq -S out.sam

But if I use the --sam-rg option i.e.:
bowtie2 --sam-rg 'ID:IL7LANE7' --local -x reference.fasta -U in.fastq -S out.sam

Then bowtie2 just exists silently, creating no output whatsover.

Does anyone know why this is happening?

I have the version "Bowtie2 2.0.0-beta5", (bowtie2-2.0.0-beta5-linux-x86_64.zip).

Thanks.
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Old 01-24-2012, 12:41 AM   #2
gringer
David Eccles (gringer)
 
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see here:

http://sourceforge.net/projects/bowt.../topic/4882702

and here, just in case the RG option doesn't do what you expect it to do:

http://sourceforge.net/tracker/index...7&atid=1101608

Also, note this from the bowtie manual:

Quote:
Note that, if any @RG fields are set using this option, the ID and SM fields must both be among them to make the @RG line legal according to the SAM Spec.
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Old 01-24-2012, 02:28 AM   #3
CHRYSES
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Quote:
Originally Posted by gringer View Post
see here:

http://sourceforge.net/projects/bowt.../topic/4882702

and here, just in case the RG option doesn't do what you expect it to do:

http://sourceforge.net/tracker/index...7&atid=1101608

Also, note this from the bowtie manual:
oh thanks a lot! I thought that gods were playing tricks on me. Apparently a known issue.

best regards
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