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pauline-ng / SIFT4G_Create_Genomic_DB

Create genomic databases with SIFT predictions. Input is an organism's genomic DNA (.fa) file and the gene annotation file (.gtf). Output will be a database that can be used with SIFT4G_Annotator.jar to annotate VCF files.
GNU General Public License v3.0
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I find a methods for speed the analysis in sift4g to build a new database #25

Closed chaimol closed 2 years ago

chaimol commented 3 years ago

when i use sift4g to build my database , I found it is very slow in use sift4g predication .

Speed up the establishment of new databases

we can add the threads in use sift4g. Only change file make-SIFT-db-all.pl line 109.just add threads before -d.

my $sift4g_command = $meta_hash{"SIFT4G_PATH"} .  " -t 24 -d " . $meta_hash{"PROTEIN_DB"} . " -q " . $meta_hash{"PARENT_DIR"} . "/all_prot.fasta --subst " .  $meta_hash{"PARENT_DIR"} . "/" . $meta_hash{"SUBST_DIR"} . " --out " .  $meta_hash{"PARENT_DIR"} . "/" . $meta_hash{"SIFT_SCORE_DIR"} . " --sub-results " ;

use -t 24 can use 24 threads to analysis ,The default threads is 8.

pauline-ng commented 2 years ago

Thank you for the tip.