Question: NCBI's blastdbcmd Error: [blastdbcmd] Entry not found: TGME49_263070 Error: [blastdbcmd] Entry or entries not found in BLAST database
1
gravatar for beckyrjb6
5 months ago by
beckyrjb610
beckyrjb610 wrote:

Hi there,

Having some trouble with NCBI's blastdbcmd... I have made the database and can run blastp successfully. I would like to now get some fasta sequences using blastdbcmd. When I run: /PATH/ncbi-blast-2.9.0+/bin/blastdbcmd -entry all -db /PATH/Tgondii_r13 -out reference.fasta

It runs perfectly and generates a file with outputs like this in it:

 >TGME49_254250 | organism=Toxoplasma_gondii_ME49 | product=PRELI family protein | location=TGME49_chrIII:1559481-1562916(-) | length=480 | sequence_SO=chromosome | SO=protein_coding
MRLFEKTFVFDSDWETVTSAFWAKYPNELQPHVLRVDTLDVDIDPEKKEFATRRLHSLKYSVPRWMECFFGGSSPVGFGL
EEAYCSLPDKVLHLKSRNYTFASFFRVDEECTYTPDPTDPSRTVYKQTATYKVFGLGAAINRALERAAVRSAEEKSSVGF
SVVQSRASSLEQQGWWGRQCAACIHSLETAAASATQHYRDLVKNLEESLHLSLSPSSPLSSPLSLERLSPSPLVESSLFA
ACAMSASAKRFLSRPSPPFVLSRNDSSSLFSLNLPFGPLSLPSLPSSLKAFLPPSSSSPSSSSSPSSPPSPSSLSLSVNA
SPPERGVFRSSGDVDCFCLRPSPGGLLPRSTLEWNRTWREERENASRRRAAIRNDSAVSSTPEEEEGPRRTDSGSSTHGA

Now i am trying to search the command:

 /Users/PATH/ncbi-blast-2.9.0+/bin/blastdbcmd -entry TGME49_254250 -db /Users/PATH/Tgondii_r13 -out TGME49_254250.fasta

It flashes up the error: Error: [blastdbcmd] Entry not found: TGME49_254250 Error: [blastdbcmd] Entry or entries not found in BLAST database

Not sure what to do! Thank you in advance for any help!

blast • 441 views
ADD COMMENTlink modified 5 months ago by Joe14k • written 5 months ago by beckyrjb610
3
gravatar for Joe
5 months ago by
Joe14k
United Kingdom
Joe14k wrote:

Did you use -parseseqids when you built the database? (cant remember the exact argument syntax).

ADD COMMENTlink written 5 months ago by Joe14k

Oh of course I completely forgot that! Thank you so much. Solved my problem :)

ADD REPLYlink written 5 months ago by beckyrjb610

Great, I've moved the post to an answer so you can accept it and provide closure to the thread :)

ADD REPLYlink written 5 months ago by Joe14k

enter image description here

ADD REPLYlink written 5 months ago by ATpoint24k
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