Question: blastn blastdbcheck errors
0
gravatar for katharp
23 months ago by
katharp0
katharp0 wrote:

Hello, I am new to linux and blast any help would be greatly appreciated. I am having trouble with the Blast nt database (blastn: 2.2.31+). I downloaded the preformatted files from NCBI using

update_blastdb.pl nt

then unzipped the files with

gunzip *.tar.gz

then used the tar function on all the respective files

tar -xv -f nt.02.tar

But when I check the database I get errors for all the files

blastdbcheck -db BLAST-DB/nt -dbtype nucl
temp/BLAST-DB/nt.50 / MetaData:   [ERROR] caught exception.
Result=FAILURE. 51 errors reported in 51 volume(s).
Testing 1 alias(es).
Result=SUCCESS. No errors reported for 1 alias(es).

Any help would be great!

Thank you,

K

blastn blast blast database • 689 views
ADD COMMENTlink modified 23 months ago by RamRS24k • written 23 months ago by katharp0

You have to run makeblastdb, first to make the alias files..

Unzipping and untar in one step:

for file in *.tar.gz; do tar -zxvf $file; done
ADD REPLYlink written 23 months ago by st.ph.n2.5k

I get another error trying to use the makeblast db

> makeblastdb -in BLAST-DB -input_type blastdb -dbtype nucl -out nt_database
>     BLAST Database error: No alias or index file found for nucleotide database [BLAST-DB] in search path [temp/BLAST-DB::]
ADD REPLYlink modified 23 months ago • written 23 months ago by katharp0
1

I thought just un-archiving the nt database files is enough to create all the files necessary.

ADD REPLYlink modified 23 months ago • written 23 months ago by genomax71k

Please format your code so it's easier to read. Use the 101010 button you see near the double quotes on the formatting bar to format your code.

ADD REPLYlink written 23 months ago by RamRS24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1963 users visited in the last hour