I am doing an alignment with bowtie2. I have paired-end files and I would like to include a .txt file for doing the alignment. By reading the manual I have found that I should use the command -12 and then the PATH for the tab-delimited .txt file. But then I get an error message:
bowtie2 --threads 4 --local --no-unal -x /home/luz_garcia_longoria/workspace/reference_genomes/parasitereference.fasta -q -k 1 --al aligned_reads.fastq -12 /home/luz_garcia_longoria/workspace/samples.txt > aligned_host_parasite.sam
Error: 1 mate files/sequences were specified with -1, but 0 mate files/sequences were specified with -2. The same number of mate files/ sequences must be specified with -1 and -2. Error: Encountered internal Bowtie 2 exception (#1) Command: /var/bin/bowtie2-2.3.1/bowtie2-align-s --wrapper basic-0 --threads 4 --local -x /home/luz_garcia_longoria/workspace/reference_genomes/parasitereference.fasta -q -k 1 -12 --passthrough /home/luz_garcia_longoria/workspace/samples.txt (ERR): bowtie2-align exited with value 1`
I also show you how my .txt file looks like:
SP1 s21 /PATH/s21_1.fq /PATH/s21_2.fq SP1 s22 /PATH/s22_1.fq /PATH/s22_2.fq SP2 s31 /PATH/s31_1.fq /PATH/s31_2.fq SP2 s32 /PATH/s32_1.fq /PATH/s32_2.fq
Is it something wrong with the .txt file?