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Old 05-05-2011, 10:49 AM   #1
Location: Wellington

Join Date: Feb 2010
Posts: 26
Default bowtie error: extra parameters specified

I am using bowtie to align short reads against a reference genome (hg19), I prepared the index of the chromosome in the ref genome and exported its location to a bin directory within bowtie as in
export HG_INDEX=/path_to_bowtie/bin/hg
so as to use it as
. Then I have the paired end short reads (about 50 bps) that I want to align and save in a sam format, so my command for running that is as follow
bowtie $HG_INDEX -q Combined.fastq -S  aligned.sam
and it generates an error as (Extra parameter(s) specified: "Combined.fastq", "aligned.sam")
So changing the command to :
bowtie $HG_INDEX -q Combined.fastq -S  --al aligned.sam
reduced the complaint to (Extra parameter(s) specified: "Combined.fastq")

I don't see any options in the bowtie switches that could enable me to avoid this error and searching around different websites looking for solution has proved futile and hence thought the SEQanswers is the best place to share this in hopes of finding a solution..

Thanks a lot
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Old 10-07-2011, 10:38 AM   #2
Location: Pittsburgh, PA

Join Date: May 2010
Posts: 22
Unhappy Extra parameter(s) specified error

I too have been getting the same error
I am running bowtie version 0.12.7 for mapping SOLiD (colorspace 50bp read length) data
against human genome (hg19), on a linux platform (CentOS). When I run with the
following parameters:

$bowtie -C -f -Q sample_QV.qual -a --best --strata -n -l 20 --maxbts --chunkmbs 1000 -t --al 50_mapped_reads.csfasta --sam -p 5 /bowtie-ref-build/hg19/hg19 sample.csfasta 50_mapping.sam
it gives me the following error

Extra parameter(s) specified: "sample.csfasta", "50_mapping.sam"

and when I was running with default seed-length(-l) value by not defining
-l 20 i.e.:

$bowtie -C -f -Q sample_QV.qual -a --best --strata -n --maxbts --chunkmbs 1000 -t --al 50_mapped_reads.csfasta --sam -p 5 /bowtie-ref-build/hg19/hg19 sample.csfasta 50_mapping.sam
it runs successfully, generating the number of reads mapped and unmapped
details on the screen.

How can I then run the program at different seed length when I run bowtie
since, as seen above, it does not run whenever I mention seed length
within permissible range (i.e. 20 > 5 for read length 50bp)?

Last edited by rahilsethi; 10-07-2011 at 10:47 AM.
rahilsethi is offline   Reply With Quote

bowtie error, extra parameters

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