Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1

Question

[salamandra]

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?

[815435542]

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

[taufiqbge]

Hello could someone please assist to resolve this error:

My command:

bowtie2-build -f NC_000913.3.fasta /home/cw2/Documents/ReferenceDB/MG1655_genome

Error: could not open NC_000913.3.fasta
Total time for call to driver() for forward index: 00:00:00
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/bin/bowtie2-build-s --wrapper basic-0 -f NC_000913.3.fasta /home/cw2/Documents/ReferenceDB/MG1655_genome

[GenoMax]

Looks like your fasta reference is not in the current directory. Provide full/relative path for a start.

[taufiqbge]

Thank you. Its done.

Answer 1

[GenoMax]

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).

Answer 2

[Levin]

try to use --threads 4 replace -p 4