I'm running this command with Bowtie2:
bowtie2 --threads 20 --no-unal -x /Path/to/Indexed/Genome/file.fna -q -k 1 --al file.fastq -U -b --align-paired-reads input.bam | samtools view -b -o output.bam
I'm getting this error message:
Error: Encountered internal Bowtie 2 exception (#1) Command: ALL My COMAND --passthrough -U -b (ERR): bowtie2-align exited with value 1
I think, the problem is that I need to use a unique input file (with paired reads inside from a previous alignment). This file is in BAM format. Reading Bowtie2 manual I found :
Reads are unaligned BAM records sorted by read name
Bowtie 2 will, by default, attempt to align unpaired BAM reads. Use this option to align paired-end reads instead.
I've read about this problem, it's related to my bowtie version? Mine is bowtie2-2.2.5.
Maybe I should try with another alignment tool? STAR ?
Thank you in advance.
PS: I've tried to run it with .SAM file (as the input) by doing:
bowtie2 --threads 20 --no-unal -x //Path/to/Indexed/Genome/file.fna -q -k 1 --al file.fastq -S no_aligned_COLL4_parasite.sam | samtools view -b -o outfile.bam