ngmaster --test returns non-zero exit status #44
Description
I installed ngmaster via conda today and --test shows an error
~$ ngmaster --test
/home/eriny/miniconda3/envs/ngmaster/lib/python3.14/site-packages/ngmaster/utils.py:11: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
from pkg_resources import resource_filename
Running ngmaster.py on test example (NG-MAST 4186 / NG-STAR 231) ...
Command '['/home/eriny/miniconda3/envs/ngmaster/bin/mlst', '--legacy', '-q', '--threads', '16', '--datadir', '/home/eriny/miniconda3/envs/ngmaster/lib/python3.14/site-packages/ngmaster/db/pubmlst', '--blastdb', '/home/eriny/miniconda3/envs/ngmaster/lib/python3.14/site-packages/ngmaster/db/blast/mlst.fa', '--scheme', 'ngmast', '--minid', '95', '--mincov', '10', '/home/eriny/miniconda3/envs/ngmaster/lib/python3.14/site-packages/ngmaster/test/test.fa']' returned non-zero exit status 2.
This is what is in my conda environment
$ conda list -n ngmaster
# packages in environment at /home/eriny/miniconda3/envs/ngmaster:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
argparse 1.4.0 pypi_0 pypi
backports.zstd 1.3.0 py314h680f03e_0 conda-forge
beautifulsoup4 4.14.3 pyha770c72_0 conda-forge
biopython 1.86 py314h5bd0f2a_0 conda-forge
blast 2.17.0 h66d330f_0 bioconda
brotli-python 1.2.0 py314h3de4e8d_1 conda-forge
bs4 0.0.2 pypi_0 pypi
bzip2 1.0.8 hda65f42_8 conda-forge
c-ares 1.34.6 hb03c661_0 conda-forge
ca-certificates 2026.1.4 hbd8a1cb_0 conda-forge
certifi 2025.11.12 pypi_0 pypi
charset-normalizer 3.4.4 pyhd8ed1ab_0 conda-forge
curl 8.17.0 h4e3cde8_1 conda-forge
entrez-direct 24.0 he881be0_0 bioconda
h2 4.3.0 pyhcf101f3_0 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 78.1 h33c6efd_0 conda-forge
idna 3.11 pyhd8ed1ab_0 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.45 default_hbd61a6d_105 conda-forge
libblas 3.11.0 5_h4a7cf45_openblas conda-forge
libcblas 3.11.0 5_h0358290_openblas conda-forge
libcurl 8.17.0 h4e3cde8_1 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.3 hecca717_0 conda-forge
libffi 3.5.2 h9ec8514_0 conda-forge
libgcc 15.2.0 he0feb66_16 conda-forge
libgcc-ng 15.2.0 h69a702a_16 conda-forge
libgfortran 15.2.0 h69a702a_16 conda-forge
libgfortran5 15.2.0 h68bc16d_16 conda-forge
libgomp 15.2.0 he0feb66_16 conda-forge
libidn2 2.3.8 hfac485b_1 conda-forge
liblapack 3.11.0 5_h47877c9_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
libmpdec 4.0.0 hb9d3cd8_0 conda-forge
libnghttp2 1.67.0 had1ee68_0 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_4 conda-forge
libsqlite 3.51.1 hf4e2dac_1 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h934c35e_16 conda-forge
libstdcxx-ng 15.2.0 hdf11a46_16 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.41.3 h5347b49_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
mlst 2.11 0 bioconda
ncbi-vdb 3.3.0 h9948957_0 bioconda
ncurses 6.5 h2d0b736_3 conda-forge
ngmaster 1.1.1 pyhdfd78af_0 bioconda
numpy 2.4.0 py314h2b28147_0 conda-forge
openssl 3.6.0 h26f9b46_0 conda-forge
pcre2 10.45 hc749103_0 conda-forge
perl 5.22.2.1 0 conda-forge
perl-archive-tar 2.18 1 bioconda
perl-bioperl 1.6.924 4 bioconda
perl-class-method-modifiers 2.11 1 bioconda
perl-common-sense 3.74 0 bioconda
perl-devel-globaldestruction 0.13 1 bioconda
perl-exporter-tiny 0.042 1 bioconda
perl-json 2.90 1 bioconda
perl-json-xs 2.34 0 bioconda
perl-list-moreutils 0.413 1 bioconda
perl-module-runtime 0.014 1 bioconda
perl-moo 2.001000 1 bioconda
perl-role-tiny 2.000001 1 bioconda
perl-sub-exporter-progressive 0.001011 1 bioconda
perl-threaded 5.32.1 hdfd78af_1 bioconda
perl-yaml 1.24 pl522_1 bioconda
pip 25.3 pyh145f28c_0 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.14.2 h32b2ec7_100_cp314 conda-forge
python_abi 3.14 8_cp314 conda-forge
readline 8.3 h853b02a_0 conda-forge
requests 2.32.5 pyhcf101f3_1 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
soupsieve 2.8.1 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_ha0e22de_103 conda-forge
typing-extensions 4.15.0 h396c80c_0 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
tzdata 2025c hc9c84f9_1 conda-forge
urllib3 2.6.2 pyhd8ed1ab_0 conda-forge
wget 1.25.0 hc2d8bac_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge