Replace abricate_exercise.md

exercises/abricate_exercise.md

@@ -10,13 +10,15 @@
 
 -   Abricate can search various databases (even custom built).
 
--   We can write a script to check which databases are installed and available using `abricate --list` 
-    We can also run that in an interactive session using the code below:
+-   We can write a script to check which databases are installed and available using `abricate --list` We can also run that in an interactive session using the code below:
 
         srun --pty -n 1 -c 2 --time=01:00:00 --mem=1G bash -l 
         module load singularityce
-        /shares/amr.imm.uzh/bioinfo/singularity/abricate_1.0.1--ha8f3691_1.sif
-        abricate --list
+        srun /shares/amr.imm.uzh/bioinfo/singularity/abricate_1.0.1--ha8f3691_1.sif abricate --list
+
+-   This will generate the following output
+
+    DATABASE SEQUENCES DBTYPE DATE card 2631 nucl 2021-Mar-27 resfinder 3077 nucl 2021-Mar-27 megares 6635 nucl 2021-Mar-27 ncbi 5386 nucl 2021-Mar-27 argannot 2223 nucl 2021-Mar-27 plasmidfinder 460 nucl 2021-Mar-27 ecoh 597 nucl 2021-Mar-27 ecoli_vf 2701 nucl 2021-Mar-27 vfdb 2597 nucl 2021-Mar-27
 
 ### Screen your genomes for resistance genes and virulence factors
 
@@ -44,3 +46,6 @@
         #SBATCH --job-name=abricate 
         #SBATCH --output=abricate\_%A\_%a.out 
         #SBATCH --error=abricate\_%A\_%a.err
+
+-   **Supplement:**
+    Screen for plasmids as well