I have a large sequence file that I want to convert into a database where I can blast other sequences against it. I've done this many times before with smaller file sizes, however this one is giving me an unclear error message:
Building a new DB, current time: 10/23/2017 14:17:46 New DB name: ~\blast\db\mydatabase New DB title: ~\blast\myseqs.fa Sequence type: Nucleotide Keep Linkouts: T Keep MBits: T Maximum file size: 1000000000B volume: ~\blast\db\mydatabase file: ~\blast\db\mydatabase.nin file: ~\blast\db\mydatabase.nhr file: ~\blast\db\mydatabase.nsq BLAST Database creation error: Need to write conversion for data type .
Note: I do not have missing residues (no empty lines), my sequences do have gaps with "-" representing gaps. I thought maybe that was the problem, but when I take say the first 10 sequences (keeping the gaps) from the same file, it converts easily into a database. So I thought maybe it was the size of the file (it is about 47400kb) so I broke the file up into 3 smaller files. Only the second file out of the three converted successfully into a nucleotide database, but the other 2 did not (note: they were all the same size and nothing was different about the sequences).
Here is the very simple command I used and have always used before with no issue:
makeblastdb.exe -in myseqs.fa -dbtype nucl -out mydatabase
I've contacted the support group for standalone blast on NCBI, but they have not responded at all to me, nor could I find any other instances of that error message on Google. I'm stumped.