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blastn blastdbcheck errors
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3.1 years ago
katharp • 0

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

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

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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.

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