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Old 06-09-2014, 05:24 PM   #1
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Default indexing the nt database with makembindex to improve blastn (task megablast) runtime

I am trying to dust mask the NT database and then to index it using makembindex. However, when I run megablast on the indexed and dust masked nt database the runtime is slower (about 3 times slower) than when I run megablast on nt without indexing. Could anyone please check the set of commands I am using? Perhaps there is an error in the parameters. I got these commands off the ncbi website's readme for megablast. Is there any way to troubleshoot why the runtime with indexing is so much slower?

Masking command:
dustmasker -in nt -infmt blastdb -parse_seqids -outfmt maskinfo_asn1_bin -out nt_dust.asnb

Merging mask data into nt:
makeblastdb -in nt -input_type blastdb -dbtype nucl -parse_seqids -mask_data nt_dust.asnb -out nt_dustmasked -title "nt"

Indexing command:
makembindex -input nt_dustmasked -iformat blastdb -old_style_index false -db_mask 11

Megablast command:
blastn -num_threads 8 -evalue 1e-30 -perc_identity 90 -word_size 45 -task megablast -outfmt 0 -show_gis -query contigs.fa -db nt_dustmasked -use_index true -db_soft_mask 11 > contigs.out 2> contigs.err
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