Question: Problem using a custom blast database in tblastx
0
gravatar for arronar
4.5 years ago by
arronar150
Austria
arronar150 wrote:

Hello.

I tried to create a custom DB for blast.

I downloaded fasta files from NCBI from an SRA project and then run this command

makeblastdb -dbtype nucl -in sra_data-DB.fasta -input_type fasta -out plant_Transcriptome_DB -title plant_Transcriptome_DB

and all seemed that went okey.

Building a new DB, current time: 06/18/2014 17:22:49
New DB name: plant_Transcriptome_DB
New DB title: plant_transcriptome_DB
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 411965 sequences in 55.2244 seconds.

Three files created. (nhr,nin,nsq)

After this, i run a test with blastdbcmd to see if everything went right.

blastdbcmd -db plant_Transcriptome_DB.nsq -info

and returned me this:

Database: plant_transcriptome_DB
411,965 sequences; 107,369,081 total bases

Date: Jun 18, 2014  5:22 PM   Longest sequence: 999 bases

Volumes:  /*/*/*/*/*/*/*/plant_Transcriptome_DB

Ok! lets run tblastx and see what is happening:

tblastx -query contig2-query.fasta -db plant_Transcriptome_DB -out output -html

Returns :

Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 2: 6, 8, 13, 33, 43-44, 47-48, 50, 55-56, 58-59, 68-70, 72, 81
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 3: 7, 16, 18, 20-22, 26-28, 30, 35, 39, 41-43, 45, 47, 49, 54, 56-57, 59-60, 63-64, 66-67, 69, 71, 79-80, 83
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 4: 7-9, 14, 16, 18, 22, 25-27, 34, 36, 41-43, 45-46, 53-55, 57, 61, 65, 67, 70, 77, 80-81, 83
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 5: 1, 7, 9, 12, 14, 16, 21, 23, 25, 30, 36, 39, 41-42, 46, 51, 53, 57, 60, 67, 69-70, 73-74, 78-79, 81-82
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 6: 1-3, 17, 21, 29, 31, 34, 38-39, 42-43, 47, 53-55, 59, 61, 63, 65-66, 72, 74-77, 79-80
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 7: 1-2, 5-8, 12-13, 16, 18, 20, 23-28, 31, 34-35, 42-45, 52, 54, 60, 62, 67, 70-71, 75-76, 78
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 8: 1, 4-5, 8-9, 16, 19, 30-32, 36, 39-42, 48, 51-52, 56-57, 62-63, 67-69, 83
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 9: 1, 5-7, 12, 14, 17, 19-22, 24-25, 27-28, 30-31, 33, 36-40, 46-47, 50-51, 54, 57-59, 63, 65, 71, 73, 75, 80-81, 83
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 10: 2-3, 5, 7, 9, 15, 17, 25-26, 31, 34, 36-39, 42, 45-47, 50, 57, 62, 64, 69, 72, 76-78
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 11: 3, 7, 10, 12, 15, 17, 23-25, 31, 33, 36-37, 39-40, 42-43, 46-47, 49, 51, 54, 56, 61-62, 66-69, 71, 73, 76, 81
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 12: 4, 9, 11, 15-17, 20-21, 26-27, 29, 34-36, 38-39, 41, 43, 46, 53-55, 66-69, 76, 78, 81
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 13: 1, 12, 16, 25-26, 29, 31, 35, 38-39, 41, 49-50, 53, 56-57, 60-62, 64-66, 70, 72-73
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 14: 1-4, 7-8, 10-11, 13-14, 18, 21-22, 27, 30-31, 35, 37, 40-41, 45, 47-49, 52-53, 57, 64, 83
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 15: 2-3, 5, 7-9, 11, 13-16, 22-24, 28-29, 35-37, 40-41, 43-44, 49, 55, 60-61, 65, 67-69, 71, 75, 78, 83
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 16: 1-3, 8-12, 15-17, 21-22, 24-25, 27, 30, 32-33, 35, 40, 43, 45, 51-52, 56, 58-60, 64, 66-68, 71-72, 75, 81, 83
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 17: 2-3, 15-16, 19, 22, 25-26, 31, 35, 38, 47-48, 51, 53, 56-59, 62-64, 67, 70-71, 76, 78-79
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 18: 2-3, 6-8, 11, 13-14, 16, 18, 26, 28, 35, 40, 43, 46-47, 50-53, 55, 58-59, 67, 69, 74, 77, 81-82
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring invalid residues at position(s): On line 19: 2, 5, 7, 11, 15, 17, 20, 22, 27, 34, 37, 40-41, 43-45, 47, 49, 52, 54-55

Any idea?

Thank you.

blast software error • 5.3k views
ADD COMMENTlink modified 12 months ago by RamRS19k • written 4.5 years ago by arronar150

I'm seeing this same thing within the Blast2GO CLI pipeline, but I've provided the blastx binary, and I'm blasting a nucleotide fasta (transcriptome) against SWISS-PROT, which is protein (swissprot.pal, etc) ... was your problem resolved by the answer below, or did it turn out to be something else?

ADD REPLYlink written 12 months ago by joseph.fass0
3
gravatar for RamRS
4.5 years ago by
RamRS19k
Houston, TX
RamRS19k wrote:

Hi,

Could you maybe give us the first few lines of the query file? I think it might be a protein and not a nucleotide query, or it might have other invalid characters. The output of `head contig2-query.fasta` would help a lot.

Thank you!

ADD COMMENTlink written 4.5 years ago by RamRS19k
1

Yes you are right! It is a protein i should try with tblastn.

>gi|573913339|ref|XP_006644353.1| PREDICTED: probable pleiotropic drug resistance protein 2-like [Oryza brachyantha]
MDTAAEMQKVASLRRGGGGSSASMWWGADNGVFSRSRSSSMAEEDDEEALRWAALEKLPTYDRVRRAILPMEGGAAAGGGEGGAGGAGGEAGKRVVDVLSLGPQERRALLERLVRVAEDDNERFLLKLKERIDRVGIDIPTIEVRFEHLEAEAEVRVGNSGLPTVL

NSMTNKFEEAGNALGIVPNRKQTMPILHDVSGVIKPRRMTLLLGPPGSGKTTLLLALAGRLNKDLKFSGQVTYNGHQMDEFVP
QRTAAYISQHDLHIGEMTVRETLAFSARCQGVGTRFDMLTELSRREKAANIKPDADIDAFMKASAMEGQETNLITDYILKILG
LEICADTMVGDDMVRGISGGQRKRVTTGEMLVGPANALFMDEISTGLDSSTTFQIVKSLRQAIHILGGTAVISLLQPAPETYD
LFDDIILLSDGQIVYQGPREGVLEFFELMGFKCPERKGVADFLQEVTSKKDQKQYWMHHEKPYRYVPVKEFAGAFQSFHTGRS
IANELATPFDKSKSHPAALTTSRYGVSAMELLKANIDREFLLMKRNSFVYIFRTCQLMVVSLIAMTLFFRTKMHRDSVTDGVI
FMGALFFSVMMIMFNGLSELPLTIFKLPVFFKQRDLLFFPAWTYTIPTWILKTPMSFIEVGGFCFMSYYVIGFDPNVGRFFKQ
YLLMLAINQMAAAMFRFVGGAARNIIVANVFGSFMLLIFMVLGGFILVREKVKKWWIWGYWISPMMYAQNAISVNEFLGHSWV

 

ADD REPLYlink written 4.5 years ago by arronar150

You're welcome!

ADD REPLYlink written 4.5 years ago by RamRS19k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2044 users visited in the last hour