Applications/Ncbi-blast - Revision history

Pysdlb: /* Batch Script */

2022-11-17T12:11:47Z

‎Batch Script

2022-11-17T12:11:26Z

‎Interactive Session

2022-11-17T12:10:57Z

‎Batch Script

2022-11-17T12:05:27Z

‎Batch Script

2022-11-17T11:59:06Z

‎SLURM Script

2022-11-16T10:53:11Z

‎Navigation

2019-05-24T13:22:53Z

2018-06-07T13:17:19Z

2017-08-23T15:24:07Z

‎Application Details

2017-04-05T13:29:25Z

Pysdlb moved page Ncbi-blast to Applications/Ncbi-blast without leaving a redirect

@@ Line 71: / Line 71: @@
 module purge
-module load ncbi-blast
+module load ncbi-blast/2.6.0
 blastp \

@@ Line 41: / Line 41: @@
 <pre style="background-color: #000; color: white; font-family: monospace, sans-serif;">
-[pysdlb@login01 ~]$ interactive
+[username@login01 ~]$ interactive
 salloc: Granted job allocation 3619736
 Job ID 3619736 connecting to c081, please wait...
 c081.vc-main
-[pysdlb@c081 ~]$ module add ncbi-blast/2.
+[username@c081 ~]$ module add ncbi-blast/2.
 ncbi-blast/2.11.0  ncbi-blast/2.12.0  ncbi-blast/2.4.0   ncbi-blast/2.6.0
-[pysdlb@c081 ~]$ module add ncbi-blast/2.6.0
+[username@c081 ~]$ module add ncbi-blast/2.6.0
 [username@c081 ~] blastp <user options>
 </pre>
 ===Batch Script===

← Older revision		Revision as of 12:10, 17 November 2022
Line 35:		Line 35:
	* update_blastdb.pl		* update_blastdb.pl
	* windowmasker		* windowmasker
		+
		+
		+	===Interactive Session===
		+
		+	<pre style="background-color: #000; color: white; font-family: monospace, sans-serif;">
		+
		+	[pysdlb@login01 ~]$ interactive
		+	salloc: Granted job allocation 3619736
		+	Job ID 3619736 connecting to c081, please wait...
		+	c081.vc-main
		+	[pysdlb@c081 ~]$ module add ncbi-blast/2.
		+	ncbi-blast/2.11.0 ncbi-blast/2.12.0 ncbi-blast/2.4.0 ncbi-blast/2.6.0
		+	[pysdlb@c081 ~]$ module add ncbi-blast/2.6.0
		+	[username@c081 ~] blastp <user options>
		+
		+	</pre>

@@ Line 43: / Line 43: @@
 #!/bin/bash
-fasta=/home/user1/maker.all.proteins.fasta
+#SBATCH -J blast
 #SBATCH -N 1
-#SBATCH --ntasks-per-node $threads_per_job
+#SBATCH --ntasks-per-node 1
 #SBATCH -o job-%j.out
 #SBATCH -e job-%j.out
 #SBATCH -p compute
-#LOAD MODULE
+# perfoms NR blast (blastx)
-module add ncbi-blast/2.4.0
+infile="$1"
+outfile="$(basename "${infile%.*}").xml"
-date
+database="/swissprot/uniprot_sprot"
-blastp -query ${p} -db $BLAST_DB -outfmt $fmt -max_target_seqs $n_seqs -culling_limit $cul -num_threads \$SLURM_NTASKS_PER_NODE -evalue $e -out ${p}-vs-nt-n$n_seqs.cul$cul.$e.blastp.out.xml
+module purge
-echo -e \"\\\nDONE\\\n\"
+blastp \
-date" > run_blastn_${p}.slurm.sh
+ -query "${infile}" \
-                sbatch run_blastn_${p}.slurm.sh
+ -db "${database}" \
-        done
+ -out "${outfile}".xml \
-        cd ..
+ -evalue 1e-5 \
-done
+ -num_threads 8 \
 </pre>

@@ Line 37: / Line 37: @@
-===SLURM Script===
+===Batch Script===
 <pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
@@ Line 99: / Line 99: @@
 </pre>
 ==Further Information==

← Older revision		Revision as of 10:53, 16 November 2022
Line 106:		Line 106:
	* [https://blast.ncbi.nlm.nih.gov/Blast.cgi https://blast.ncbi.nlm.nih.gov/Blast.cgi]		* [https://blast.ncbi.nlm.nih.gov/Blast.cgi https://blast.ncbi.nlm.nih.gov/Blast.cgi]

−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

@@ Line 106: / Line 106: @@
 * [https://blast.ncbi.nlm.nih.gov/Blast.cgi https://blast.ncbi.nlm.nih.gov/Blast.cgi]
-{|
+==Navigation==
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

@@ Line 2: / Line 2: @@
 * Description: NCBI-Blast finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
-* Version: 2.4.0
+* Version: 2.4.0 , 2.6.0
-* Modules: ncbi-blast/2.4.0
+* Modules: ncbi-blast/2.4.0, ncbi-blast/2.6.0
 * Licence: Open-source (BLAST is a registered trademark of the National Library of Medicine)

← Older revision	Revision as of 13:29, 5 April 2017
(No difference)