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?