Question: converting a fasta database to blastp database
0
gravatar for maxpayneb13
6.1 years ago by
Portugal
maxpayneb130 wrote:

hello im runnnig a wwwblast software on my server i do have a fasta database and i would like to use it in wwwblast

i googled it a little and found that " makeblastdb " does the job i used this command to convert my database  :

makeblastdb -in Iraller3.fasta -dbtype 'prot' -out iraller_db

i gives me this output :

New DB name:   iraller_db
New DB title:  Iraller3.fasta
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Adding sequences from FASTA; added 1706 sequences in 0.0759079 seconds.

 

so i modified the main index.html on wwwblast and added the database name to the list :

<select name = "DATALIB">
    <option VALUE = "iraller"> iraller database 
    <option VALUE = "test_aa_db"> test_aa_db
</select>

and the files are in the db folder , but when i try to search a query i get this error : 

The combination of database and program, that you provided in your
message is invalid or not acceptable by BLAST search system.
Please look at current possible combinations in BLAST help.

 

this is the contents of the db folder : 

CDD  Iraller3.fasta    iraller_dbls.pin  iraller_db.phr  iraller_db.psq  iraller.pin  test_aa_db      test_aa_db.pin  test_aa_db.pni  test_aa_db.psi  test_na_db      test_na_db.nin
CVS  iraller_dbls.phr  iraller_dbls.psq  iraller_db.pin  iraller.phr     iraller.psq  test_aa_db.phr  test_aa_db.pnd  test_aa_db.psd  test_aa_db.psq  test_na_db.nhr  test_na_db.nsq

sorry if my question is a little long i was trying to give all the details

thanks

blast • 3.0k views
ADD COMMENTlink modified 5.6 years ago by thackl2.8k • written 6.1 years ago by maxpayneb130

Could not quite understand your question. Check if your sequences are nucleotide or protein. If nucleotide use -dbtype 'nucl', otherwise use -dbtype 'prot'. From this page, it seems that if your database is created using BLAST+ 2.2.29 version, you can just safely ignore the errors as it seems to be a bug in the software.

ADD REPLYlink written 6.1 years ago by Prakki Rama2.4k
0
gravatar for rtliu
6.0 years ago by
rtliu2.1k
New Zealand
rtliu2.1k wrote:

Have a try:

 <option VALUE = "iraller_db"> iraller database 
ADD COMMENTlink written 6.0 years ago by rtliu2.1k
0
gravatar for thackl
5.6 years ago by
thackl2.8k
MIT
thackl2.8k wrote:

Just for closure: this was fixed in BLAST+ 2.2.30 according to http://blastedbio.blogspot.de/2014/04/error-1431-fasta-reader-ignoring-modifiers.html.

ADD COMMENTlink written 5.6 years ago by thackl2.8k
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