GPU blast - k821209/pipelines GitHub Wiki

nr database to gpu format db

#bindir = ~/programs/gpu-blast-1.1_ncbi-blast-2.2.28/ncbi-blast-2.2.28+-src/c++/GCC480-ReleaseMT64/bin/
$ $bindir/makeblastdb -in ./nr -out ./sorted_nr -sort_volumes -input_type blastdb -dbtype prot -max_file_sz 200MB
# max file size를 조절하면 메모리 문제를 해결할 수 있다 메모리 킬이 나면 줄이자.

실행

$ gpu_blastp -db ../db/sorted_nr -query best_candidates.pep -gpu t -method 2
$ gpu_blastp -db db -query input.fa -gpu t -evalue 1e-5 -outfmt 7 -num_alignments 1 -out out.ev1e5.out