Question: I need help to fix this script, it runs nicely but gives error message that i am not able to fix.
0
gravatar for Nano
4.1 years ago by
Nano20
Finland
Nano20 wrote:

`~/Documents/Blast/makeblastdb -in Bmori.fst -dbtype nucl -out Bmori_BlastDB -parse_seqids`; ## Creating Bmori database

$BLAST_DB='Bmori_BlastDB'; ## storing in a variable

@QUERY_FILES=`ls *.fas`; ## list all the transcriptomes of different species

foreach $tmp (@QUERY_FILES)
{
        #print "$tmp";
        chomp($tmp); ##remove new line character 
`/appl/bio/blast/2.2.31/bin/blastn -query $tmp -db $BLAST_DB -out $tmp\_vs\_$BLAST_DB.txt -evalue 0.01 -outfmt 6`; ## blast version 2.2.25 command
}

 

Error messge: BLAST Database error: No alias or index file found for nucleotide database [Bmori_BlastDB.psq] in search path [/homeappl/home/shuezu/transcriptomes:/proj/csc/biosci/biodb/production/blast:]

 

blast gene • 1.2k views
ADD COMMENTlink modified 4.1 years ago by Jean-Karim Heriche21k • written 4.1 years ago by Nano20
0
gravatar for Jean-Karim Heriche
4.1 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

Check the name of your database file, in particular, check that the name you're passing to blastn has the same suffix as the file on disk. You must use the name of the file you ran formatdb on. A common mistake is to use the name of the index file created by formatdb, e.g. if you formatted the file sequences.fa with formatdb -i sequences.fa -p F, you should also have sequences.fa.nhr, sequences.fa.nin and sequences.fa.nsq and the name of the database used by blastn will be sequences.fa.

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Jean-Karim Heriche21k
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