(ERR): "GRCh38_noalt_as" does not exist or is not a Bowtie 2 index Exiting now ...

Question

[Song]

Hi All,

I've been struggling with trying to align my fastq files to the Bowtie Indexed human genome. I followed this tutorial https://www.metagenomics.wiki/tools/short-read/remove-host-sequences and am now stuck where bowtie doesn't recognize the indexed database that I downloaded, which is a ready to use bowtie2 databse.

Here is my shell script:

#!/bin/bash
#SBATCH --nodes=1   # number of nodes
#SBATCH --ntasks-per-node=8   # 16 processor core(s) per node X 2 threads per core
#SBATCH --mem=500G   # maximum memory per node
#SBATCH --partition=mem   # standard node(s)
#SBATCH --job-name=%j
#SBATCH --mail-user=[e-mail]   # email address
#SBATCH --mail-type=BEGIN
#SBATCH --mail-type=END
#SBATCH --mail-type=FAIL
#SBATCH --output=%j.out# job standard output file (%j replaced by job id)
#SBATCH --error=%j.err # job standard error file (%j replaced by job id) date                       

cd /project/metagenomics_of_retail_poultry/20230920/trimmed_fastq/trimmed_files

module load bowtie2/2.5.2

bowtie2 -p 8 -x GRCh38_noalt_as -1 1-446345050_R1.trim.fastq -2 1-446345050_R2.trim.fastq --very-sensitive-local --un-conc-gz
--reorder SAMPLE_host > 1-446345050_mapped_and_unmapped.sam

I keep getting this error:

(ERR): "GRCh38_noalt_as" does not exist or is not a Bowtie 2 index
Exiting now ...

I have inspected the bowtie2 index and it looked fine.

Any help will be greatly appreciated! Thank you!

Answer 1

[Ram]

-x needs the full prefix to the index files. Did you do the wget + unzip steps in that tutorial in the same folder (/project/metagenomics_of_retail_poultry/20230920/trimmed_fastq/trimmed_files) that you're in right now? If not, provide the full path to the place where you did the wget and unzip.

[Song]

I figured it out and found my mistake! I had to specify the folder and basename, for example GRCh38_noalt_as/GRCh38_noalt_as