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Old 03-04-2014, 11:45 AM   #1
Location: Walnut, California

Join Date: Dec 2012
Posts: 39
Default Blast 'makeblastdb' Error: (1431.1)


I am creating a database for a 2.7Gb merged sequences that I have, but I get the following error:

command used: /usr/local/bin/makeblastdb -in Merged_Lsat_1_v4.fa -dbtype nucl -parse_seqids

Building a new DB, current time: 03/04/2014 19:26:23
New DB name: Merged_Lsat_1_v4.fa
New DB title: Merged_Lsat_1_v4.fa
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 50% ambiguous nucleotides (shouldn't be over 40%)

Does anyone have a workaround or any suggestions on what I can do to fix this problem? blast doesnt quit after the error message, it just hangs in there.

Thank you,

milo0615 is offline   Reply With Quote
Old 03-04-2014, 02:06 PM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

Is the warning correct (do you have lots of IUPAC ambiguity codes instead of just A,C,G,T)?

If not, it could be a sign that there was an error interpreting your FASTA file.
maubp is offline   Reply With Quote
Old 03-04-2014, 03:07 PM   #3
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,992

If Merged_Lsat_1_v4.fa was edited on a PC/Mac and then moved to a UNIX server then this could be an indication of the file format (PC/Mac vs UNIX) problem.
GenoMax is offline   Reply With Quote
Old 03-14-2014, 01:11 PM   #4
Naibin Duan
Junior Member
Location: ithaca

Join Date: Jan 2014
Posts: 3

I also have this proble ,but I got the answer ,you should check your file :Merged_Lsat_1_v4.fa.

there must be nnnnnnnnnnnnnnnnnn....... in it ,Good luck !
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Old 05-16-2014, 08:56 AM   #5
Location: Davis, CA

Join Date: May 2011
Posts: 53

I blogged about this very topic yesterday:

It is not a great 'error' message'. Actually, it's a warning message that also has 'Error' pre-pended to it. It only looks at the first line of your sequence to determine this. So if you the same amount of Ns at the end of the sequence, you won't see the error.

So it's mostly harmless, and a little pointless. You will see that message if your first line has >40% ambiguous characters even if

a) the first line is only 5 bp
b) the rest of the entire sequence is free from ambiguity codes
kbradnam is offline   Reply With Quote
Old 01-20-2015, 08:37 AM   #6
Location: Switzerland

Join Date: Aug 2013
Posts: 41

But does it essentially add the sequence to the database and (real warning) ,
or does it skip this sequence (error)? It isnt really conclusive to me
ebioman is offline   Reply With Quote
Old 01-20-2015, 06:46 PM   #7
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

My interpretation of the message is this is a warning only, and the sequence was still added to the database.

You can check this using blastdbcmd (either look at the total number of sequences, or use this tool to extract FASTA sequences from the database for an in depth check).
maubp is offline   Reply With Quote

blast, error:1431.1, fasta-reader, makeblastdb

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