command line - Blast+ Local Configuration: How to configure nt and nr databases? -


i configuring blast+ on mac (os sierra) , having trouble configuring nr , nt databases downloaded locally. trying follow ncbi's instructions here, , getting hung on configuration , example execution steps.

they change .bash_profile says:

export path=$path:$home/documents/luke/research/pedulla\ 17-18/blast/ncbi-blast-2.6.0+/bin

that works fine, , configure path blastdb "similarly" file db be, have done this:

export blastdb=$blastdb:$home/documents/luke/research/pedulla\ 17-18/blast/blastdb/nt.00

which specifies exact folder got when unzipped nt tar file ftp. path, if run command...

blastn -query test_query.fa -db nt.00 -task blastn -outfmt "7 qseqid sseqid evalue bitscore" -max_target_seqs 5

then runs , results, worried these being checked against nt.00 section of entire nt.00 database file, because if run test_query.fa sequence on web blast, different results.

also, instructions path needs point folder contains whole database folder nt.00, tar unzipped--and not specific nt.00 itself--, in case "blastdb/" (as opposed "blastdb/nt.00/" contains nt.00.nhd, nt.00.nal, etc.). makes sense because when working want able blastn on nt database blastp on nr one, etc. changing -db flag on command, , there shouldn't problem having them in folder, right? if must specify path blastdb nt.00 db added end, how ever use nr.00 in same folder (blastdb/)? essentially, want instructions say, , have this:

export blastdb=$blastdb:$home/documents/luke/research/pedulla\ 17-18/blast/blastdb/

and depending on database want use after -db flag on command. when make path above, gives me error: 

blast database error: no alias or index file found nucleotide database [nt] in search path [/users/ljstout::/users/ljstout/documents/luke/research/pedulla 17-18/blast/blastdb:]

i have tried running same blastn command above , swapping out "nt" "nt.00", , have tried these commands path blastdb ending in both "blastdb/" , "blastdb/nt" , of course "blastdb/nt.00" 1 runs without errors.

here's example of thread read op worried executions not checking entire nt.00 folder, different problem however.

thanks help!

this whole problem came down having nt.00 & nr.00 files, original folders result unzipping respective .tar.gz's, in same parent folder when should their contents in same parent folder. deleted folders came in , copied contents on new, singular parent. kind of mislead instructions, simple mistake. now, have 1 folder, blastdb/ contains of contents of every database plan on using, including nt,nr, , refseq.


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