I am trying to use bowtie for the first time and I get a constant error about the options that I have put to the command. I leave the script.
bowtie2 --threads 4 --local --no-unal -x /home/luz_garcia_longoria/workspace/referencegenome/sturnus_relictumgenome.fasta -q -k 1 --al aligned_reads.fastq -U /home/luz_garcia_longoria/workspace/*.fq > aligned_host_parasite.sam
Warning: Output file '/home/luz_garcia_longoria/workspace/s22_2.fq' was specified without -S. This will not work in future Bowtie 2 versions. Please use -S instead.
Extra parameter(s) specified: "/home/luz_garcia_longoria/workspace/s23_1.fq", "/home/luz_garcia_longoria/workspace/s23_2.fq", "/home/luz_garcia_longoria/workspace/s24_2.fq", "/home/luz_garcia_longoria/workspace/s25_1.fq", "/home/luz_garcia_longoria/workspace/s25_2.fq", "/home/luz_garcia_longoria/workspace/s31_1.fq", "/home/luz_garcia_longoria/workspace/s31_2.fq", "/home/luz_garcia_longoria/workspace/s32_1.fq", "/home/luz_garcia_longoria/workspace/s32_2.fq", "/home/luz_garcia_longoria/workspace/s33_1.fq", "/home/luz_garcia_longoria/workspace/s34_1.fq", "/home/luz_garcia_longoria/workspace/s34_2.fq", "/home/luz_garcia_longoria/workspace/s35_1.fq", "/home/luz_garcia_longoria/workspace/s35_2.fq"
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/referencegenome/sturnus_relictumgenome.fasta -q -k 1 --passthrough -U /home/luz_garcia_longoria/workspace/s22_1.fq /home/luz_garcia_longoria/workspace/s22_2.fq /home/luz_garcia_longoria/workspace/s23_1.fq /home/luz_garcia_longoria/workspace/s23_2.fq /home/luz_garcia_longoria/workspace/s24_2.fq /home/luz_garcia_longoria/workspace/s25_1.fq /home/luz_garcia_longoria/workspace/s25_2.fq /home/luz_garcia_longoria/workspace/s31_1.fq /home/luz_garcia_longoria/workspace/s31_2.fq /home/luz_garcia_longoria/workspace/s32_1.fq /home/luz_garcia_longoria/workspace/s32_2.fq /home/luz_garcia_longoria/workspace/s33_1.fq /home/luz_garcia_longoria/workspace/s34_1.fq /home/luz_garcia_longoria/workspace/s34_2.fq /home/luz_garcia_longoria/workspace/s35_1.fq /home/luz_garcia_longoria/workspace/s35_2.fq
(ERR): bowtie2-align exited with value 1
If I include the -S option, the same error keeps appearing and if I delete the -U option and include -S then I get the same error but starting from the file s23_1.
I do not know if it is important but the files have a link to another folder, that is, they are not really in the folder where I am indicating they are. But I know that normally it works like this so as not to "damage" the original files.
I hope someone can help me.