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Old 10-15-2015, 11:05 AM   #1
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Location: Bay Area, California

Join Date: Oct 2015
Posts: 5
Default makeblastdb is making multiple sets of files, how can I fix it?


I just realized I should have posted this to this forum, so here it is again, sorry!

I am a graduate student at UC Berkeley currently working with raw reads of several transcriptomes in an attempt to find and assemble reads that match a couple of genes I'm studying. This site has already been very useful to me (Thank you!!!!), but I haven't found any answers pertaining to my current problem.

I was hoping I could get some help with a BLAST problem I'm having. I am working with standalone blast, and am building blast databases from fasta files of transcriptome raw reads. I have successfully used the command:

makeblastdb -in COST_1_final.fasta -input_type fasta -dbtype nucl -out COST_1_final for several fasta files of raw reads (with varying names of course) but a few of the files result in multiple sets of database files, marked for example <filename>.00.nhr and <filename>.01.nhr with what I believe is an alias file <filename>.nal

The command as it runs give the usual message:
Building a new DB, current time: 10/15/2015 10:49:55
New DB name: COST_u_final
New DB title: COST_u_final.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 16313457 sequences in 937.429 seconds.

but then results in multiple sets of files.

Any ideas about how I can make just one set of database files, as has successfully happened with the rest of my fasta files? I would really appreciate any help!!
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Old 10-15-2015, 11:14 AM   #2
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Solved here:

Last edited by GenoMax; 10-15-2015 at 11:35 AM.
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