Bwa-mem2 indexing not working down stream

Question

[mgranada3]

I am using bwa-mem2 to create my index and to map my reads to the reference genome.

This is my indexing code

#!/bin/bash
#SBATCH -J index
#SBATCH -A gts-rro3
#SBATCH -N 1 --ntasks-per-node=24
#SBATCH --mem-per-cpu=8G
#SBATCH -t 1:00:00
#SBATCH -o index.out

cd $SLURM_SUBMIT_DIR
ml intel/20.0.4
export PATH=/storage/home/programs/bwa-mem2:$PATH

bwa-mem2 index -p index CgGenome_chromosomes.fasta.gz

I get 5 files as an output and no error in my outfile.

However, when I continue downstream to map my first read I get this error: "ERROR! Unable to open the file: /storage/home/scratch/BwaMem/index.bwt.2bit.64"

I am assuming the problem is starting at the indexing step but I have tried reinstalling bwa-mem2 on our cluster and re-running the complier. Any insight on what could be going on?

[ATpoint]

Please show code for the downstream analysis. Did the indexing succeed properly, anything odd in the logs? How big is the genome in terms of basepairs.

[mgranada3]

About 13k bp. I suspect the indexing never worked. I have seen some posts saying that indexing takes a long time but mine takes like 10 seconds.

Downstream code to use bwa-mem2 to map reads:

#!/bin/bash
#SBATCH -J aligntest
#SBATCH -A gts-rros3
#SBATCH -N 1 --ntasks-per-node=24
#SBATCH --mem-per-cpu=8G
#SBATCH -t 1:00:00
#SBATCH -o align_test.out

cd $SLURM_SUBMIT_DIR
ml intel/20.0.4
export PATH=/storage/programs/bwa-mem2:$PATH

bwa-mem2 mem -t 24 /index /FR04_0_S1.paired1.fq.gz /FR04_0_S1.paired2.fq.gz -o FR04_SC_0.sam

Links edited to remove my school information