Differences

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--- alphafold2 [2024/03/13 09:28] – created Luc Bonnefond
+++ alphafold2 [2024/03/18 16:04] (current) – Luc Bonnefond
@@ Line 16: / Line 16: @@
 #!/bin/bash
 #SBATCH --mail-type=ALL
-#SBATCH --mail-user=username@igbmc.fr
+#SBATCH --mail-user=Your_email
 #SBATCH --cpus-per-task 2
 #SBATCH --gres=gpu:a3g.20gb:1
@@ Line 24: / Line 24: @@
 module load alphafold/2.3.2
 AF=/shared/genomes/alphafold2/2023-04-28
 srun run_alphafold.sh \
     --data_dir=$AF/ \
-    --output_dir=$(pwd)/ap_out \
+    --output_dir=$(pwd)/ap_out_Your_Result_Directory \
-    --fasta_paths=sequence.fasta \
+    --fasta_paths=Your_Sequence_File.fasta \
     --max_template_date=2020-05-14 \
     --db_preset=full_dbs \
@@ Line 44: / Line 43: @@
 <code>
 #!/bin/bash
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=Your_email
+#SBATCH --cpus-per-task 2
+#SBATCH --gres=gpu:a3g.20gb:1
+#SBATCH --mem=100G
 #SBATCH -p gpu
-#SBATCH --gres=gpu:a3g.20gb:1
+#SBATCH -t 8-00:00:00
-#SBATCH --cpus-per-task=10
-#SBATCH --mem=50G
-#SBATCH --mail-user=username@igbmc.fr
-#SBATCH --mail-type=ALL
 module load alphafold/2.3.2
-mkdir -p /tmp/username
 AF=/shared/genomes/alphafold2/2023-04-28
 srun run_alphafold.sh \
     --data_dir=$AF/ \
-    --output_dir=$(pwd)/ap_out \
+    --output_dir=$(pwd)/ap_out_Your_Result_Directory \
-    --fasta_paths=TOP2A_HUMAN_DIMER.fasta \
+    —fasta_paths=Your_Multiple_Sequence_File.fasta \
     --max_template_date=2020-05-14 \
     --db_preset=full_dbs \
@@ Line 74: / Line 69: @@
     --pdb_seqres_database_path=$AF/pdb_seqres/pdb_seqres.txt \
     --uniprot_database_path=$AF/uniprot/uniprot.fasta
 </code>
+Run the script:
+<code>sbatch xxx.sh</code>
+You will get one email when the job start and a second one when its complete (or crashed). You can also follow it with <quote>''squeue''</quote>