Annotation

Use Diamond to annotate the predicted genes

Source the configuration file:

source conf_cluster.conf

Run Blast alignment using Diamond:

diamond blastp --query $GENE_PRED/prodigal.idba.$PRJ_NAME.faa \
--db $DB/nr \
-o $GENE_PRED/diamond.prodigal.idba.$PRJ_NAME.m8 \
--sensitive

Alternatively, prepare a script for a batch submission.

Create a new script file:

nano Diamond.sh

Copy and paste the following test into the file Diamond.sh:

#!/bin/bash

cd $SLURM_SUBMIT_DIR
source conf_cluster.conf

echo "`date`: Diamond blast starts"

diamond blastp --query $GENE_PRED/prodigal.idba.$PRJ_NAME.faa \
--db $DB/nr \
-o $GENE_PRED/diamond.prodigal.idba.$PRJ_NAME.m8 \
--sensitive -p 12

echo "`date`: Diamond blast ends"

and make it executable:

chmod a+x Diamond.sh

Exit from inteactive job:

exit

and submit the script:

sbatch -p gll_usr_prod --account train_embo2018 --reservation=s_tra_embo2018 --time 24:00:00 --mem=28000 -N 1 -n 12 ./Diamond.sh

Have a look to the submitted job:

squeue -u <username>

Have a look to the results:

cd $GENE_PRED
ll
less diamond.prodigal.idba.$PRJ_NAME.m8