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2 hours ago by

I'm struggling to add rg-id to alignments. I use the command below

bowtie2 -p 10 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /home/ptaklifi/genome_folder/rCRSd/bowtie2_index/default/rCRSd —-rg-id SRR10984461 --un-conc mt/un-seqs.fastq -1 SRR10984461_1-trimmed-pair1.fastq -2 SRR10984461_1-trimmed-pair2.fastq

which gives this error message:

Warning: Output file '—-rg-id' was specified without -S.  This will not work in future Bowtie 2 versions.  Please use -S instead.
Extra parameter(s) specified: "SRR10984461"
Note that if <mates> files are specified using -1/-2, a <singles> file cannot
also be specified.  Please run bowtie separately for mates and singles.
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/bin/bowtie2-align-s --wrapper basic-0 -p 10 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /home/ptaklifi/genome_folder/rCRSd/bowtie2_index/default/rCRSd --passthrough -1 SRR10984461_1-trimmed-pair1.fastq -2 SRR10984461_1-trimmed-pair2.fastq —-rg-id SRR10984461 
(ERR): bowtie2-align exited with value 1

somehow bowtie2 thinks --rg-id is the output. I checked bowtie2 manual and I believe --rg-id <text> specifies rg id.
Any suggestions how to solve this ?
thank you

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