Bowtie2 error with single end mapping

Question

[H.Hasani]

Dear all,

I'm facing a tedious error and not sure what causing it. I have single-end reads and simply trying to align it using Bowtie2 as follows:

bowtie2 -p 10 --sensitive --no-mixed -t -x my_genome -U my_File.fq.gz -S my_output.sam

When I print this line, everything seems correct, however, Bowtie2 terminates with the following error:

bowtie2-2.2.6/bin/bowtie2-align-s --wrapper basic-0 -p 10 --sensitive --no-mixed -t -x my_genome -S my_output.sam -U /tmp/11841.unp

I forgot to mention the input is completely fine, as I checked it with zcat and it is indeed a correct fastq format.

Can somebody explain this to me and what should I do?

Thanx

[GenoMax]

I think you forgot to include information about the error (i.e. include more lines around where you are seeing this).

[Rohit]

Not sure why you are using --no-mixed with single end reads though, -U option must take care of single end reads

[Devon Ryan]

1. What's your actual error? I'm guessing something to do with truncated input.
2. If you send me the path on slack I can have a look.

[H.Hasani]

Thank you all. I realized that bowtie2 was not able to access the genome folder.

Answer 1

[Lakshman Teja]

Hello, You Just try the below command

bowtie2 -x bowtie_index -U read.fastq -S alignment.sam --no-unal