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)
Use the biobuilds channel to get the correct perl version:
I had to create a new conda environment to make sure down-grading perl didn’t mess with other dependencies.
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?