There is a problem with the BLASTN xml output
Based on biojava, I personally made and am using something that works with blastN.
I was using the NR and NT DB of v4 locally. However, there was one problem after updating this v5.
I tried to read and xml the pasta file with version 2.11.0 of BLAST+. (This is for Excel parsing.)
It works well in the database of v4, but v5 doesn't give me the results. (0 bytes)
The following are the options I used.
[blastn, , -task, megablast,
-db, db_loc
-query, C:\Users\Cosmos\Desktop\report.fas,
-num_threads, 4,
-num_alignments, 10,
-num_descriptions, 10,
-out, C:\Users\Cosmos\Desktop\blast.xml,
-outfmt, 5]
Is there anything I haven't checked?
I look forward to your advice.
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What is the error you get (if any) ?
Don't know specifically for the xml output but lots has changed from v4 to v5 ... might be worth looking into the change logs of the BLAST binaries (or DBs) .
the problem that occurs to me is... In v4, normal xml content is output to the command line above, but If I change only the NT file of v5 and use it, only the xml file is created and there is no content (0bytes). and no error(s). I will definitely look at the changes. Thank you for your advice.
After thinking about it all night, I found out that I did something different than usual. When downloading from ftp server. Instead of update_blast.pl file, I downloaded the file using the ftp server subordinate program. Can this be a problem?