Error: Encountered internal Bowtie 2 exception (#1)

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

bowtie2

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updated 2.1 years ago by GenoMax

• written 2.1 years ago by gabriel •

enter image description here

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written 2.1 years ago by gabriel •

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

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updated 2.1 years ago by GenoMax

• written 2.1 years ago by gabriel •

1 answer

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

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written 2.1 years ago by GenoMax

Thank you, that was it

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written 2.1 years ago by gabriel •

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