Question: magicblast aganist local nr database
1
gravatar for Assa Yeroslaviz
4 weeks ago by
Assa Yeroslaviz1.4k
Munich
Assa Yeroslaviz1.4k wrote:

I have downloaded the complete nr datadase to my local server. I have now a list of nr.00* to nr.38*

nr.00.phd
nr.00.phi
nr.00.phr
nr.00.pin
nr.00.pog
nr.00.ppd
nr.00.ppi
nr.00.psq
nr.00.tar.gz.md5
nr.01.phd
...
nr.38.ppd
nr.38.ppi
nr.38.psq
nr.38.tar.gz.md5
nr.pal
nr.pdb
nr.pos
nr.pot
nr.ptf
nr.pto
taxdb.btd
taxdb.bti

I would like now to run magicblast against this local data base, but I keep getting the error massage, I don't have an index file.This is the command I am trying to run:

$magicblast -query R2_val_2.tagged_filter.fastq.gz  -db /home/BLASTdb/nr -infmt fastq -outfmt tabular -num_threads 5 -out WK56.R2.unmapped.magicblast.nr.txt

I am getting this error

BLAST Database error: No alias or index file found for nucleotide database [/home/BLASTdb/nr] in search path [/local/projects/Chad/P286::]

Can someone tell me what I am doing wrong? Do I need to somehow combine these files?

thanks

blast magicblast nr local • 108 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Assa Yeroslaviz1.4k
1

magicblast is only meant for use against DNA databases.

ADD REPLYlink written 4 weeks ago by genomax92k

I know, I wanted to run it against the nt database, not nr.

ADD REPLYlink written 4 weeks ago by Assa Yeroslaviz1.4k

Hello Assa Yeroslaviz!

We believe that this post does not fit the main topic of this site.

I have downloaded the nr database, which is the non redundant protein database, but I need nt!

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 4 weeks ago by Assa Yeroslaviz1.4k

Heed this warning from magicblast help page. Trying to map against nt will not be a good idea.

Magic-BLAST can also work with a genome as a FASTA file. However it is not recommended for more than a few million bases, because mapping to a FASTA file is much slower than to a BLAST database.

ADD REPLYlink written 4 weeks ago by genomax92k

But I don't have a FASTA file.

I have a BLAST DB, splitted into several files

hence the 00, 01, etc.

nr.00.phd
nr.00.phi
nr.00.phr
nr.00.pin
nr.00.pog
nr.00.ppd
nr.00.ppi
nr.00.psq

Or do I miss something?

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Assa Yeroslaviz1.4k

Documentation for magicblast only refers to using a (one) genome/transcriptome (or at most a few SRA accessions). Let us know if using the nt blast database works. As you said above you will replace nr with nt database.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by genomax92k
1
gravatar for Assa Yeroslaviz
28 days ago by
Assa Yeroslaviz1.4k
Munich
Assa Yeroslaviz1.4k wrote:

yes it does.

my command was as such

magicblast -query  tagged_filter.fastq.gz  -db BLASTdb/nt/nt -infmt fastq -outfmt tabular -num_threads 5 -out unmapped.magicblast.nt.txt

while the folder with the data base is as such

$ ls -1 BLASTdb/nt
nt.00.nhd
nt.00.nhi
nt.00.nhr
nt.00.nin
nt.00.nnd
nt.00.nni
nt.00.nog
nt.00.nsq
nt.00.tar.gz.md5
nt.01.nhd
nt.01.nhi
...
nt.27.tar.gz.md5
nt.nal
nt.ndb
nt.nos
nt.not
nt.ntf
nt.nto
taxdb.btd
taxdb.bti
ADD COMMENTlink written 28 days ago by Assa Yeroslaviz1.4k
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