Question: Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
0
gravatar for salamandra
21 months ago by
salamandra180
salamandra180 wrote:

I'm trying to run bowtie2.

These are the commands:

UNMAP=/pathtofile/unmappedreads.txt
BWTID=/pathtofile/btw2index/hg19
READS=/pathtofile/merged.fastq
OUTPUT=/pathtofile/merged.SAM
bowtie2 -p 4 —un $UNMAP —no-unal -x $BWTID -U $READS -S $OUTPUT

I get this error:

Extra parameter(s) specified: "—un", "/pathtofile/unmappedreads.txt", "—no-unal"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/local/bin/../Cellar/bowtie2/2.2.4/bin/bowtie2-align-s --wrapper basic-0 -p 4 -x /pathtofile/btw2index/hg19 -S /pathtofile/merged.SAM -U /pathtofile/merged.fastq —un /pathtofile/unmappedreads.txt —no-unal 
(ERR): bowtie2-align exited with value 1

Could please someone help?

chip-seq • 5.6k views
ADD COMMENTlink modified 5 months ago by 8154355420 • written 21 months ago by salamandra180

if this problem is not solved until now, you can remove the "-p 4" and try again.

ADD REPLYlink written 5 months ago by 8154355420
1
gravatar for genomax
21 months ago by
genomax62k
United States
genomax62k wrote:

Some bowtie2 options are specified with -- (two hyphens). Unless your terminal converted those to a single smarthyphen that would be first place to start (--un and --no-unal).

ADD COMMENTlink modified 21 months ago • written 21 months ago by genomax62k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2075 users visited in the last hour