kat comp never exits - bioconda only issue(?)

[chrisgulvik]

I haven't tested install from src, so this might just be a bioconda issue. I wanted to post in case others run into this.

The help menus exit just fine, but this creates all output files as-expected and even stdout shows "KAT COMP completed." but oddly never exits even after 1+ hour. As a temporary workaround, this solution works: (timeout 1m kat comp --output_prefix kat <( zcat *.fq.gz ) asm.fna; exit 0)

Here are expected outfiles:

3.0K    kat.dist_analysis.json
2.0M    kat-main.mx
93K     kat-main.mx.spectra-cn.png
1.0K    kat.stats

Below is how I installed it in conda:

conda create -n kat2.4.2 kat -c bioconda -y

Here are the pkgs it installed:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
boost-cpp                 1.70.0               ha2d47e9_1    conda-forge
brotli                    1.1.0                hd590300_1    conda-forge
brotli-bin                1.1.0                hd590300_1    conda-forge
brotli-python             1.1.0            py38h17151c0_1    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
ca-certificates           2024.8.30            hbcca054_0    conda-forge
certifi                   2024.8.30          pyhd8ed1ab_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.5            py38hdb19cb5_0
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
dbus                      1.13.18              hb2f20db_0
expat                     2.6.2                h59595ed_0    conda-forge
fontconfig                2.14.1               hef1e5e3_0
fonttools                 4.53.1           py38h2019614_0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
glib                      2.78.4               h6a678d5_0
glib-tools                2.78.4               h6a678d5_0
gst-plugins-base          1.14.1               h6a678d5_1
gstreamer                 1.14.1               h5eee18b_1
icu                       58.2              hf484d3e_1000    conda-forge
idna                      3.8                pyhd8ed1ab_0    conda-forge
importlib_resources       6.4.4              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
kat                       2.4.2            py38hfc5f9d8_2    bioconda
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4            py38h6a678d5_0
krb5                      1.20.1               h81ceb04_0    conda-forge
lcms2                     2.12                 h3be6417_0
ld_impl_linux-64          2.40                 hf3520f5_7    conda-forge
lerc                      3.0                  h295c915_0
libblas                   3.9.0           20_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hd590300_1    conda-forge
libbrotlidec              1.1.0                hd590300_1    conda-forge
libbrotlienc              1.1.0                hd590300_1    conda-forge
libcblas                  3.9.0           20_linux64_openblas    conda-forge
libclang                  10.0.1          default_hb85057a_2
libdeflate                1.17                 h5eee18b_1
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libevent                  2.1.12               hf998b51_1    conda-forge
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc                    14.1.0               h77fa898_1    conda-forge
libgcc-ng                 14.1.0               h69a702a_1    conda-forge
libgfortran               14.1.0               h69a702a_1    conda-forge
libgfortran-ng            14.1.0               h69a702a_1    conda-forge
libgfortran5              14.1.0               hc5f4f2c_1    conda-forge
libglib                   2.78.4               hdc74915_0
libgomp                   14.1.0               h77fa898_1    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
liblapack                 3.9.0           20_linux64_openblas    conda-forge
libllvm10                 10.0.1               he513fc3_3    conda-forge
libopenblas               0.3.25          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.39               h5eee18b_0
libpq                     12.17                hdbd6064_0
libstdcxx                 14.1.0               hc0a3c3a_1    conda-forge
libstdcxx-ng              14.1.0               h4852527_1    conda-forge
libtiff                   4.5.1                h6a678d5_0
libwebp-base              1.4.0                hd590300_0    conda-forge
libxcb                    1.16                 hb9d3cd8_1    conda-forge
libxkbcommon              1.0.1                hfa300c1_0
libxml2                   2.9.14               h74e7548_0
lz4-c                     1.9.4                hcb278e6_0    conda-forge
matplotlib                3.7.2            py38h06a4308_0
matplotlib-base           3.7.2            py38h1128e8f_0
munkres                   1.0.7                      py_1    bioconda
ncurses                   6.5                  he02047a_1    conda-forge
nspr                      4.35                 h27087fc_0    conda-forge
nss                       3.89.1               h6a678d5_0
numpy                     1.24.4           py38h59b608b_0    conda-forge
openjpeg                  2.5.2                he7f1fd0_0
openssl                   3.3.2                hb9d3cd8_0    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pcre2                     10.42                hebb0a14_1
pillow                    10.4.0           py38h5eee18b_0
pip                       24.2               pyh8b19718_1    conda-forge
platformdirs              4.2.2              pyhd8ed1ab_0    conda-forge
ply                       3.11               pyhd8ed1ab_2    conda-forge
pooch                     1.8.2              pyhd8ed1ab_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.10          py38h6a678d5_0
pyqt5-sip                 12.13.0          py38h5eee18b_0
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.8.19               h955ad1f_0
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python_abi                3.8                      2_cp38    conda-forge
qt-main                   5.15.2               h327a75a_7
readline                  8.2                  h8228510_1    conda-forge
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
scipy                     1.10.1           py38h59b608b_3    conda-forge
setuptools                73.0.1             pyhd8ed1ab_0    conda-forge
sip                       6.7.12           py38h17151c0_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.45.3               h5eee18b_0
tabulate                  0.9.0              pyhd8ed1ab_1    conda-forge
tk                        8.6.14               h39e8969_0
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.4.1            py38hfb59056_0    conda-forge
unicodedata2              15.1.0           py38h01eb140_0    conda-forge
urllib3                   2.2.2              pyhd8ed1ab_0    conda-forge
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xz                        5.4.6                h5eee18b_1
zipp                      3.20.1             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h5eee18b_1
zstd                      1.5.5                hc292b87_2