Can't locate @INC


Roary suddenly stopped working (see message below). I used it last week and everything went smoothly, since then I do not recall to install or update anything. Uninstall and install roary again gives the same error. I would be very grateful if you can assist me with this.

It happened at GVL
~$ roary
Can’t locate Bio/Roary/CommandLine/ in @INC (you may need to install the Bio::Roary::CommandLine::Roary module) (@INC contains: /home/ubuntu/lib /home/ubuntu/miniconda2/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi /home/ubuntu/miniconda2/lib/perl5/site_perl/5.22.0 /home/ubuntu/miniconda2/lib/perl5/5.22.0/x86_64-linux-thread-multi /home/ubuntu/miniconda2/lib/perl5/5.22.0 .) at /usr/local/bin/roary line 12.
BEGIN failed–compilation aborted at /usr/local/bin/roary line 12.

Thank you,

The problem is miniconda2 - do you have any miniconda environments active while trying to run roary?

Hi @mattbull, thanks for prompt reply!
I didnt create, not activate any extras. How else can i check it?
$ conda list

packages in environment at /home/ubuntu/miniconda2:

Name Version Build Channel

asn1crypto 0.24.0 py27_0
biopython 1.68 py27_0 bioconda
blast 2.2.31 1 bioconda
boost 1.65.1 py27_4
bwa 0.7.17 pl5.22.0_2 bioconda
bzip2 1.0.6 h9a117a8_4
ca-certificates 2018.4.16 0 conda-forge
certifi 2018.4.16 py27_0 conda-forge
cffi 1.11.4 py27h9745a5d_0
chardet 3.0.4 py27hfa10054_1
conda 4.4.10 py27_0
conda-env 2.6.0 h36134e3_1
cryptography 2.1.4 py27h6697b16_0
curl 7.60.0 0 conda-forge
drmaa 0.7.8 py27_0
enum34 1.1.6 py27h99a27e9_1
freebayes 1.2.0 htslib1.7_0 bioconda
freetype 2.8 hab7d2ae_1
futures 3.2.0 py27h7b459c0_0
htslib 1.7 0 bioconda
icu 58.2 h9c2bf20_1
idna 2.6 py27h5722d68_1
intel-openmp 2018.0.0 8
ipaddress 1.0.19 py27_0
java-jdk 8.0.92 1 bioconda
jpeg 9b h024ee3a_2
krb5 1.14.6 0 conda-forge
libboost 1.65.1 habcd387_4
libedit 3.1 heed3624_0
libffi 3.2.1 hd88cf55_4
libgcc 7.2.0 h69d50b8_2
libgcc-ng 7.2.0 h7cc24e2_2
libgfortran-ng 7.2.0 hdf63c60_3
libpng 1.6.34 hb9fc6fc_0
libssh2 1.8.0 2 conda-forge
libstdcxx-ng 7.2.0 h7a57d05_2
libtiff 4.0.9 h28f6b97_0
mkl 2018.0.2 1
mkl_fft 1.0.1 py27h3010b51_0
mkl_random 1.0.1 py27h629b387_0
mmtf-python 1.0.2 py27_0 bioconda
msgpack-python 0.5.6 py27h6bb024c_0
ncurses 6.0 h9df7e31_2
neptune 1.2.5 py27_1 bioconda
numpy 1.14.2 py27hdbf6ddf_1
olefile 0.45.1 py27_0
openssl 1.0.2o 0 conda-forge
parallel 20170422 pl5.22.0_0 bioconda
perl 0 conda-forge
perl-app-cpanminus 1.7043 pl5.22.0_0 bioconda
perl-bioperl 1.6.924 4 bioconda
perl-exporter-tiny 0.042 1 bioconda
perl-file-slurp 9999.19 0 bioconda
perl-list-moreutils 0.428 pl5.22.0_0 bioconda
perl-threaded 5.22.0 pl5.22.0_12 bioconda
perl-time-piece 1.27 pl5.22.0_0 bioconda
perl-yaml 1.24 0 bioconda
pillow 5.0.0 py27h3deb7b8_0
pip 9.0.1 py27ha730c48_4
py-boost 1.65.1 py27hf484d3e_4
pycosat 0.6.3 py27ha4109ae_0
pycparser 2.18 py27hefa08c5_1
pyopenssl 17.5.0 py27hcee3be0_0
pysocks 1.6.7 py27he2db6d2_1
python 2.7.14 h1571d57_29
readline 7.0 ha6073c6_4
reportlab 3.4.0 py27_0
requests 2.18.4 py27hc5b0589_1
ruamel_yaml 0.15.35 py27h14c3975_1
samtools 1.7 1 bioconda
scipy 1.0.1 py27hfc37229_0
setuptools 38.4.0 py27_0
six 1.11.0 py27h5f960f1_1
snippy 3.2 pl5.22.0_1 bioconda
snpeff 4.3 3 bioconda
sqlite 3.22.0 h1bed415_0
tk 8.6.7 hc745277_3
urllib3 1.22 py27ha55213b_0
vcflib 1.0.0_rc1 1 bioconda
vcftools 0.1.15 1 bioconda
wheel 0.30.0 py27h2bc6bb2_1
xz 5.2.3 h55aa19d_2
yaml 0.1.7 had09818_2
zlib 1.2.11 ha838bed_2

conda info --envs

conda environments:

base * /home/ubuntu/miniconda2

OK - the problem is that miniconda adds itself to the PATH during installation (you can say yes or no, but it defaults yes!).

If you check the bottom of ~/.bashrc, you’ll find a line added by miniconda that is something like:


If you comment this line out using a text editor (like nano or vi) to read:

# PATH=/home/ubuntu/miniconda2/bin

Then log out and back in again to reset your PATH, does this make roary more happy?


Thanks a lot, works like a charm!

All the best!

1 Like

Remember that when you want to use miniconda, you’ll need to uncomment that line and log out and back in again!

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.