# "Install_dependencies.pl" gives "Aborted" when downloading "nr" database?

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"Install_dependencies.pl" gives "Aborted" when downloading "nr" database?
#1
Downloading nr.96.tar.gz... [OK]
Downloading nr.97.tar.gz... [OK]
Downloading nr.98.tar.gz... [OK]
Downloading nr.99.tar.gz... [OK]
Aborting....
Aborted!


Dear Friends - when running "install_dependencies.pl", I get this above error when the script downloads nr database. I ran the script thrice but it gives the same error. Could you please let me know how to solve this issue? The command line I ran is:

./install_dependencies.pl standard &> log.log &

Thanks

Post Situation:
Sat, 2019-09-14 08:53
Danielsebas

Hello,

I'm not sure what could cause this, perhaps your version of the install_dependencies.pl script is not new enough?  which version of distributed rosetta are you using?

~Dan

Sun, 2019-09-15 10:04
danpf

Thanks! I am using the latest one from the website "rosetta_src_2019.31.60840_bundle.tgz". I have used the same rosetta bundle on my ubuntu 18.04 and it worked all well with no issues. But when running the same script on centos 6.9, I am gettign this error. Any idea how this can be resolved?

Mon, 2019-09-16 09:28
Danielsebas

herm sorry I've never used centos before, I'm not really sure what could be the issue.

the problem appears to occur in the 'update_blast' part of the script, so you could go to the databases folder in fragment_tools, and try running

perl databases/update_blastdb.pl nr

and maybe you will get a little bit more information?

unfortuantely this is provided to us from the ncbi so i'm not sure if there are any fancy requirements for it.

when we run this we do so in a conda environment which has:

conda channels you should add:
- bioconda
- compbiocore

conda packages:
- perl
- perl-if
- perl-parallel-forkmanager
- perl-switch
- perl-text-balanced
- perl-json

(before running make sure you)

export PERL5LIB="\$(wherever your conda environment is)/lib/site_perl/5.26.2/"



if you don't know conda very well, then it might be best to ignore the above advice and to try installing perl-switch and perl-parallel-forkmanager from your operating system

(maybe there's an easy way to do that in centos?)

Mon, 2019-09-16 09:51
danpf