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
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:
Below is how I installed it in conda:
Here are the pkgs it installed: