Question: How to update nr database for commandline BLAST?
0
gravatar for tcf.hcdg
15 months ago by
tcf.hcdg60
European Union
tcf.hcdg60 wrote:

I downloaded the nr databaselast year (nr00.tar.gz-nr61.tar.gz) and now would like to update the ne database as now they are up to nr90.tar.gz.

I tried to use the updatae script but encounter the following error:

tb44227@lido-gw02:~/nobackup/ncbi-blast-2.6.0+/db/nrdb>perl update_blastdb.pl nr --passive
Can't locate Archive/Tar.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at update_blastdb.pl line 42.
BEGIN failed--compilation aborted at update_blastdb.pl line 42.

Does anyone have idea how to fix this?

Another thing I would like to ask: Is it also possible to doenload only the files which were not avaialable previously like the files from nr62.tar.gz to nr90.tar.gz rather than updating?

blast update database • 1.1k views
ADD COMMENTlink written 15 months ago by tcf.hcdg60

For now I would say, just remove everything and execute the update script. I thought it already was that it downloads new files and also update. You always need to update everything.

you may need to update your perl. https://stackoverflow.com/questions/47801223/how-to-fix-cant-locate-archive-tar-pm

ADD REPLYlink written 15 months ago by gb1.0k

I believe the update_blastdb.pl script should do what you want, and only download files that are missing/need updating.

It looks like a problem with your perl install as @gb said.

ADD REPLYlink written 15 months ago by Joe14k

Yes I did same but the same error:

tb44227@lido-gw01:~/nobackup/ncbi-blast-2.6.0+/db/nrdb>update_blastdb.pl

Can't locate Archive/Tar.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at ./update_blastdb.pl line 42. BEGIN failed--compilation aborted at ./update_blastdb.pl line 42.s

ADD REPLYlink written 15 months ago by tcf.hcdg60
1

In the terminal:

cpan -i Archive::Tar

Also check your perl version:

perl -v
ADD REPLYlink written 15 months ago by gb1.0k
1

That might fix it. Tar has been included as standard in Perl for a while now though, so this would suggest that the version of perl in use is just very out of date.

The more 'robust' solution, would probably be the latest version of perl installed from scratch.

Unless of course there are compatibility issues that would break a load of things if it was upgraded, which is very possible in the world of bioinformatics!

ADD REPLYlink written 15 months ago by Joe14k

Yes that's the same error. Perl is telling you what the problem is:

Can't locate Archive/Tar.pm in @INC

Perl is missing a library in its include path for dealing with tar-ed files. You need to reinstall or update perl. Googling your error finds the exact same stackoverflow thread that @gb found.

Just follow that thread through.

ADD REPLYlink written 15 months ago by Joe14k
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