bioconda-recipes: prokka: "Can't locate Bio/Root/Version.pm" error

@Slugger70 I’m running prokka 1.13 2 bioconda, and am getting the following error:

Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module) (@INC contains: /ebio/abt3_projects/methanogen_host_evo/bin/llga-lr/.snakemake/conda/126413bc/bin/../perl5 /ebio/abt3_projects/methanogen_host_evo/bin/llga-lr/.snakemake/conda/126413bc/lib/site_perl/5.26.2/x86_64-linux-thread-multi /ebio/abt3_projects/methanogen_host_evo/bin/llga-lr/.snakemake/conda/126413bc/lib/site_perl/5.26.2 /ebio/abt3_projects/methanogen_host_evo/bin/llga-lr/.snakemake/conda/126413bc/lib/5.26.2/x86_64-linux-thread-multi /ebio/abt3_projects/methanogen_host_evo/bin/llga-lr/.snakemake/conda/126413bc/lib/5.26.2 .) at /ebio/abt3_projects/methanogen_host_evo/bin/llga-lr/.snakemake/conda/126413bc/bin/prokka line 32.

Here’s the full conda env:

aragorn                   1.2.38               h470a237_2    bioconda
barrnap                   0.9                           1    bioconda
bedtools                  2.27.1               he941832_2    bioconda
blast                     2.7.1                h96bfa4b_5    bioconda
boost                     1.66.0                   py36_1    conda-forge
boost-cpp                 1.66.0                        1    conda-forge
bzip2                     1.0.6                h470a237_2    conda-forge
ca-certificates           2018.4.16                     0    conda-forge
certifi                   2018.4.16                py36_0    conda-forge
expat                     2.2.5                hfc679d8_1    conda-forge
gmp                       6.1.2                hfc679d8_0    conda-forge
gnutls                    3.5.19               h2a4e5f8_1    conda-forge
hmmer                     3.2                  hfc679d8_3    bioconda
icu                       58.2                 hfc679d8_0    conda-forge
infernal                  1.1.2                h470a237_1    bioconda
java-jdk                  8.0.92                        1    bioconda
libffi                    3.2.1                         3    conda-forge
libgcc                    7.2.0                h69d50b8_2
libgcc-ng                 7.2.0                hdf63c60_3
libgfortran-ng            7.2.0                hdf63c60_3
libidn11                  1.33                          0    conda-forge
libopenblas               0.2.20               h9ac9557_7
libstdcxx-ng              7.2.0                hdf63c60_3
minced                    0.2.0                         0    bioconda
ncurses                   6.1                  hfc679d8_1    conda-forge
nettle                    3.3                           0    conda-forge
numpy                     1.14.3           py36h28100ab_2
numpy-base                1.14.3           py36h0ea5e3f_1
openssl                   1.0.2o               h470a237_1    conda-forge
parallel                  20160622                      1    bioconda
pcre                      8.41                 h470a237_2    conda-forge
perl                      5.26.2               h470a237_0    conda-forge
perl-app-cpanminus        1.7044                  pl526_1    bioconda
perl-archive-tar          2.18                    pl526_3    bioconda
perl-bioperl              1.6.924                       4    bioconda
perl-carp                 1.38                    pl526_1    bioconda
perl-compress-raw-bzip2   2.074           pl526hfc679d8_0    bioconda
perl-compress-raw-zlib    2.069           pl526ha92aebf_7    bioconda
perl-constant             1.33                    pl526_1    bioconda
perl-exporter             5.72                    pl526_1    bioconda
perl-exporter-tiny        1.000000                pl526_0    bioconda
perl-extutils-makemaker   7.34                    pl526_0    bioconda
perl-file-path            2.15                    pl526_0    bioconda
perl-file-temp            0.2304                  pl526_2    bioconda
perl-io-compress          2.069           pl526hfc679d8_5    bioconda
perl-io-zlib              1.10                    pl526_2    bioconda
perl-list-moreutils       0.428                   pl526_1    bioconda
perl-list-moreutils-xs    0.428                   pl526_0    bioconda
perl-parent               0.236                   pl526_1    bioconda
perl-pathtools            3.73                 h470a237_2    bioconda
perl-scalar-list-utils    1.45            pl526h470a237_3    bioconda
perl-test-more            1.001002                pl526_1    bioconda
perl-threaded             5.22.0                       13    bioconda
perl-xml-namespacesupport 1.12                    pl526_0    bioconda
perl-xml-parser           2.44            pl526h3a4f0e9_5    bioconda
perl-xml-sax              1.00                    pl526_0    bioconda
perl-xml-sax-base         1.09                    pl526_0    bioconda
perl-xml-sax-expat        0.51                    pl526_2    bioconda
perl-xml-simple           2.22                    pl526_1    bioconda
perl-xsloader             0.24                    pl526_0    bioconda
perl-yaml                 1.26                    pl526_0    bioconda
pip                       18.0                     py36_1    conda-forge
prodigal                  2.6.3                         1    bioconda
prokka                    1.13                          2    bioconda
python                    3.6.6                h5001a0f_0    conda-forge
readline                  7.0                  haf1bffa_1    conda-forge
setuptools                40.0.0                   py36_1    conda-forge
sqlite                    3.24.0               h2f33b56_0    conda-forge
tbl2asn                   25.6                          3    bioconda
tk                        8.6.8                         0    conda-forge
wheel                     0.31.1                   py36_1    conda-forge
xz                        5.2.4                h470a237_0    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge

About this issue

  • Original URL
  • State: closed
  • Created 6 years ago
  • Comments: 22 (17 by maintainers)

Most upvoted comments

Use the biobuilds channel to get the correct perl version:

conda install -c biobuilds perl=5.22

I had to create a new conda environment to make sure down-grading perl didn’t mess with other dependencies.

conda install -c biobuilds perl=5.22

I’m running into the same issue and unfortunately, it didn’t fix the error. Does that still persist? Any other solutions?

I am experiencing this very same issue! I installed prokka via conda, and tried all the above fixes but to no avail:

Can’t locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module)

Any ideas? Do I need different versions of dependencies / Prokka? Install a different way?