ERROR: bowtie2 align exited with value 1

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5.2 years ago

anastasia.gs17 • 0

Hey, I am trying to map some seq data with bowtie2, using this command:

bowtie2 --threads 12 -x /metagenomics/anastasia/data_release/raw_data/Bowtie2_mapping/final_contigs.index -1 /metagenomics/anastasia/data_release/raw_data/Pf11_1_clean.fq  -2 /metagenomics/anastasia/data_release/raw_data/Pf11_2_clean.fq -S /metagenomics/anastasia/data_release/raw_data/Bowtie2_mapping/Pf11.sam  --no-unal

and I keep getting this error: (ERR): bowtie2-align exited with value 1 I have been using bowtie2 for a while now and everything was fine, this is the first time that this is happening to me. Does anyone know what kind of error is that?

Anastasia

next-gen alignment • 3.6k views

ADD COMMENT • link updated 5.2 years ago by GenoMax 141k • written 5.2 years ago by anastasia.gs17 • 0

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Output of ls /metagenomics/anastasia/data_release/raw_data/Bowtie2_mapping/ ?

ADD REPLY • link 5.2 years ago by ATpoint 81k

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An exit status of 1 is a general indicator that something went wrong, but it doesn't tell you what.

I'm probably running an old version of bowtie, but I don't see a --no-unal option. Does your command run successfully without it?

ADD REPLY • link 5.2 years ago by Joe 21k

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