Blastn cannot open .nin files

PlutonicFriend

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Join Date: Jun 2012

Posts: 2
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#1

Blastn cannot open .nin files

07-23-2012, 06:28 PM

I am having problems with my standalone blast databases.
I have made them in the past and they have worked however now when I try to blastn against them i get a warning such that:
[blastall] WARNING: Unable to open ATGTCA1db.00.nin
[blastall] WARNING: Unable to open ATGTCA1db.00.nin
[blastall] WARNING: Unable to open ATGTCA1db.00.nin
[blastall] WARNING: Unable to open ATGTCA1db.00.nin
[blastall] WARNING: Unable to open ATGTCA1db.01.nin
[blastall] WARNING: Unable to open ATGTCA1db.01.nin
[blastall] WARNING: Unable to open ATGTCA1db.01.nin
[blastall] WARNING: Unable to open ATGTCA1db.01.nin
[blastall] WARNING: Unable to open ATGTCA1db.02.nin
[blastall] WARNING: Unable to open ATGTCA1db.02.nin
[blastall] WARNING: Unable to open ATGTCA1db.02.nin
[blastall] WARNING: Unable to open ATGTCA1db.02.nin
etc.

When I look at the out put of creating the databast it has been made correctly as far as I can tell:
New DB name: BlastLib/ATGTCA1db
New DB title: ATGTCA1.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1073741824B
Adding sequences from FASTA; added 40083681 sequences in 6226.41 seconds.

and the code I'm using to blast againt the file is:
blastall -p blastn -i LuciMatch -d /iob_home/dwhlab/behrimg/SarahHiSeq/ATGTCA1/BlastLib/ATGTCA1db -o ./BlastResults/ATG_Luc_Elong

I dont really know what is going wrong. Any help would be appreciated I'm getting very frustrated.
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cliffbeall

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Join Date: Jan 2010

Posts: 144
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#2

07-24-2012, 12:37 PM

I would check that the path to the "BlastLib" directory is correct and those .nin files are there and have those exact names.

If its neither of those, maybe you need to change permissions?
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Blastn cannot open .nin files

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