Error: Encountered internal Bowtie 2 exception (#1)

Question

[gabriel]

I'm trying to run an analysis but when I use the command it gives me the bowtie information with this message at the end

 Command: /usr/bin/bowtie2-align-s --wrapper basic-0 -x reference/index/Osativa -u fastq/D0DTNACXX_1_fastq_fastqc.gz -s --threads 8 
(ERR): bowtie2-align exited with value 1

[gabriel]

[gabriel]

bowtie2 -x reference/index/Osativa -u fastq/D0DTNACXX_1_fastq_fastqc.gz -s mapped.sam --threads 8

Answer 1

[GenoMax]

Run the command using bowtie2. Provide a file name to hold the output with option -S (capital). -s is for something else.

[gabriel]

Thank you, that was it