Differences

This shows you the differences between two versions of the page.

--- blast_and_plast [2021/09/02 16:11] – 38.20.199.40
+++ blast_and_plast [2024/11/04 10:14] (current) – 110.239.172.216
@@ Line 10: / Line 10: @@
 cd $PWD
 CPUs=10
-DB=/db1/nr-nt-fasta-oct-2020/nt
+DB=/scratch3/rogerlab_databases/other_dbs/nr_March252023/plast/nr.fasta
 QF=yourquery.fasta
-plast -e 1e-10 -max-hit-per-query 1 -outfmt 1 -a $CPUs -p plastn -max-database-size 10000000000 -i $QF -d $DB -o $QF.plout -force-query-order 1000
+plast -e 1e-10 -max-hit-per-query 1 -outfmt 1 -a $CPUs -p plastp -max-database-size 10000000000 -i $QF -d $DB -o $QF.plout -force-query-order 1000
 </code>
-to parse the output see http://129.173.88.134:81/dokuwiki/doku.php?id=dayana_salas_-_utility_scripts_taxonomy_coloring_trees_phylogenetics_mixture_models_domain_architecture_and_more
+to parse the output see https://perun.biochem.dal.ca/user-wiki/doku.php?id=taxonomy_recovery
@@ Line 26: / Line 26: @@
 #$ -S /bin/bash
 . /etc/profile
-#$ -pe threaded 1
+#$ -pe threaded 10
 #$ -cwd
 source activate blast
-export BLASTDB=/db1/nr-nt-oct-2020-v5/
+export BLASTDB=/db1/blast-may-2024/
 DB=nt
 query=your_query.fasta
-blastn -db $DB -query $query -out yourqueryresults.blout -num_threads 1 -outfmt "6 qseqid sseqid evalue pident qcovs length slen qlen qstart qend sstart send stitle"
+blastn -db $DB -query $query -out yourqueryresults.blout -num_threads 10 -outfmt "6 qseqid sseqid evalue pident qcovs length slen qlen qstart qend sstart send stitle"
-source deactivate
+conda deactivate
 </code>
-Both shells using NCBI nt database (/db1/nr-nt-jan-2019/nt.nal), but the formats for specifying DB are different for BLAST and PLAST.
+Both shells use NCBI nt database, but PLAST doesn't support new v5 NCBI nr and nt databases and can cause Segmentation fault error.
+<Last updated by Dandan Zhao on Jun 11, 2024>