Question: Error "Can't locate List/MoreUtils.pm in @INC"
0
gravatar for mckf11111
9 months ago by
mckf1111120
mckf1111120 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 • 2.0k views
ADD COMMENTlink modified 9 months ago by genomax51k • written 9 months ago by mckf1111120
0
gravatar for h.mon
9 months ago by
h.mon16k
Brazil
h.mon16k 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 9 months ago by h.mon16k

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 9 months ago by mckf1111120
0
gravatar for Istvan Albert
9 months ago by
Istvan Albert ♦♦ 77k
University Park, USA
Istvan Albert ♦♦ 77k 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 9 months ago • written 9 months ago by Istvan Albert ♦♦ 77k
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