Closed:bowtie2 alignment error
0
0
Entering edit mode
3.1 years ago
pt.taklifi ▴ 60

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

alignment • 236 views
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 1588 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6