I am trying to run the following batch script using slurm. However, I am running to the problem by getting the ExitCode 127.
#!/bin/bash
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=1
#SBATCH --mem=200gb
#SBATCH -t 24:00:00
#SBATCH --mail-type=ALL
#SBATCH [email protected]
#SBATCH -p wdsp
#SBATCH -o qiime2_Sepp.out
#SBATCH -e qiime2_Sepp.err
## Load the relevant modules needed for the job
#module purge
#module load miniconda3
#conda activate qiime2-amplicon-2024.10
#conda init
#source ~/.bashrc
export TMPDIR=/tmp/
## Run script
qiime.sh
I am getting the following error:
/var/spool/slurmd/job12345/slurm_script: line 25: qiime.sh: command not found
Here is the qiime.sh
:
#!/bin/bash
cd ~/SEPP/
# importing data
echo 'Importing Data ...'
qiime tools import \
--input-path rep_seqs.fna \
--output-path rep-seqs.qza \
--type "FeatureData[Sequence]"
# SEPP Tree construction
echo 'SEPP Tree construction ...'
qiime fragment-insertion sepp \
--i-representative-sequences rep-seqs.qza \
--i-reference-database sepp-refs-silva-128.qza \
--p-threads 50 \
--p-debug \
--o-tree tree-sepp-new.qza \
--o-placements inser-plac-sepp.qza
Is there something obvious that I am missing here? I will appreciate any help and advice.