Blast 'makeblastdb' Error: (1431.1)

[milo0615]

Hello,

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,

-Milo

[maubp]

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.

[GenoMax]

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.

[Naibin Duan]

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 !

[kbradnam]

I blogged about this very topic yesterday:

http://www.acgt.me/blog/2014/5/15/fun-with-an-error-message-from-ncbi-blast

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

[ebioman]

Hi
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

[maubp]

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).