Question: Error "Can't locate List/MoreUtils.pm in @INC"
0
gravatar for Wenhu_Cao
2.1 years ago by
Wenhu_Cao50
Wenhu_Cao50 wrote:

Hi,

I encoutered some technical problem when learning BLAST in the HANDBOOK as below:

After I use conda install blast to install ncbi-blast, and run the command:

**update_blastdb.pl --decompress 16SMicrobial**

the shell complains:

**Can't locate List/MoreUtils.pm in @INC (you may need to install the List::MoreUtils module) (@INC contains: /etc/perl /usr/loc
al/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/li
b/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /home/mck
f111/miniconda3/envs/bioinfo/bin/update_blastdb.pl line 43.**

Could anyone tell me how to fix this? Thanks a lot!

blast • 6.0k views
ADD COMMENTlink modified 2.1 years ago by genomax74k • written 2.1 years ago by Wenhu_Cao50
1
gravatar for Istvan Albert
2.1 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

it looks like the conda installation does not list a dependency for the tool. This should fix it:

conda install perl-list-moreutils

I will make the change in the book.

Since this perl package normally is included on most Unix system it does not show up on most systems.

In addition the update_ blastdb.pl script tries makes use of a hardcoded perl version rather than the environment so you may need to use

 perl `which update_blastdb.pl`

(note the backticks)

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Istvan Albert ♦♦ 81k

great answer, I just add some alternative solution to your last command line:

To force update_blastdb.pl to use your environment perl instead of the local one you can simply edit the first line of the "update_blastdb.pl" file changing this:

#!/usr/bin/perl

into this:

#!/usr/bin/env perl
ADD REPLYlink modified 14 months ago • written 14 months ago by rgiannico110
0
gravatar for h.mon
2.1 years ago by
h.mon28k
Brazil
h.mon28k wrote:

Use cpan or cpanm to install the List::MoreUtils module:

cpanm List::MoreUtils

Depending on your system, you may need to be root. If that is the case, you may install Perl on the same conda environment as you installed Blast, then install the module with cpan or cpanm.

ADD COMMENTlink written 2.1 years ago by h.mon28k

I have run this command, and it shows several distributions has been installed. However, when I run update_blastdb.pl --decompress 16SMicrobial

the shell still complains:

Can't locate List/MoreUtils.pm in @INC (you may need to install the List::MoreUtils module) (@INC contains: /etc/perl /usr/loc al/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/li b/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /home/mck f111/src/ncbi-blast-2.7.0+/bin/update_blastdb.pl line 43. BEGIN failed--compilation aborted at /home/mckf111/src/ncbi-blast-2.7.0+/bin/update_blastdb.pl line 43. (bioinfo)

ADD REPLYlink written 2.1 years ago by Wenhu_Cao50
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