Sketchlib back end not available?

[hayleyjaywilson]

Versions Poppunk V2.6.0 poppunk_sketch --version respectively. Alternatively, please post the output of conda list in your environment -->

Command used and output returned poppunk --create-db --r-files reference_list.txt --output strain_db --threads 8 --plot-fit 5

error: mash: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory Sketchlib backend not availableNeed mash v2 or higher

Describe the bug I am not sure what has happened. I followed the install instructions for the pp_env - so a fresh environment. I have tried updating python, pp_sketchlib and poppunk but no joy. But the software will not run even if I attempt to manually install.

Also poppunk_sketch --version returns: -bash: poppunk_sketch: command not found

I am not sure what the issue with the install is (apologies if it is obvious)

Many thanks

[johnlees]

How did you install PopPUNK, can you copy the commands you ran?

[hayleyjaywilson]

Hi thanks for the quick reply

Conda create -n pp_env poppunk python=3.8

[johnlees]

Can you also give the output of conda list?

[hayleyjaywilson]

My environment is c alled poppunk_env rather than pp_env.

conda list (poppunk_env) @.*** ~]$ conda list

packages in environment at /home/hjw58/.conda/envs/poppunk_env:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge aom 3.5.0 h27087fc_0 conda-forge at-spi2-atk 2.38.0 h0630a04_3 conda-forge at-spi2-core 2.40.3 h0630a04_0 conda-forge atk-1.0 2.38.0 hd4edc92_1 conda-forge biopython 1.81 py38h1de0b5d_0 conda-forge boost 1.78.0 py38h4e30db6_4 conda-forge boost-cpp 1.78.0 h6582d0a_3 conda-forge brotli 1.0.9 h166bdaf_9 conda-forge brotli-bin 1.0.9 h166bdaf_9 conda-forge brotli-python 1.0.9 py38hfa26641_9 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.19.1 hd590300_0 conda-forge ca-certificates 2023.05.30 h06a4308_0 cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.16.0 hbbf8b49_1016 conda-forge cairomm-1.16 1.16.2 h7e731d7_1 conda-forge certifi 2023.5.7 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py38h4a40e3a_3 conda-forge charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge contourpy 1.1.0 py38h7f3f72f_0 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge cython 3.0.0 py38h17151c0_0 conda-forge dav1d 1.2.1 hd590300_0 conda-forge dbus 1.13.18 hb2f20db_0 dendropy 4.6.1 pyhdfd78af_0 bioconda docopt 0.6.2 py_1 conda-forge epoxy 1.5.10 h166bdaf_1 conda-forge expat 2.5.0 hcb278e6_1 conda-forge ffmpeg 6.0.0 gpl_hdbbbd96_103 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.41.0 py38h01eb140_0 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge gdk-pixbuf 2.42.10 h6b639ba_2 conda-forge gettext 0.21.1 h27087fc_0 conda-forge glib 2.76.4 hfc55251_0 conda-forge glib-tools 2.76.4 hfc55251_0 conda-forge gmp 6.2.1 h58526e2_0 conda-forge gnutls 3.7.8 hf3e180e_0 conda-forge graph-tool 2.57 py38h7041675_0 conda-forge graph-tool-base 2.57 py38h327f3be_0 conda-forge graphite2 1.3.14 h295c915_1 gtk3 3.24.38 hf583ffa_0 conda-forge h5py 3.8.0 nompi_py38hd5fa8ee_100 conda-forge harfbuzz 7.3.0 hdb3a94d_0 conda-forge hdbscan 0.8.33 py38h31356c5_0 conda-forge hdf5 1.12.2 nompi_h4df4325_101 conda-forge hicolor-icon-theme 0.17 ha770c72_2 conda-forge icu 72.1 hcb278e6_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge importlib-resources 6.0.0 pyhd8ed1ab_1 conda-forge importlib_resources 6.0.0 pyhd8ed1ab_1 conda-forge joblib 1.3.0 pyhd8ed1ab_1 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.4 py38h43d8883_1 conda-forge krb5 1.21.1 h659d440_0 conda-forge lame 3.100 h166bdaf_1003 conda-forge lcms2 2.15 haa2dc70_1 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libaec 1.0.6 hcb278e6_1 conda-forge libass 0.17.1 hc9aadba_0 conda-forge libblas 3.9.0 17_linux64_openblas conda-forge libbrotlicommon 1.0.9 h166bdaf_9 conda-forge libbrotlidec 1.0.9 h166bdaf_9 conda-forge libbrotlienc 1.0.9 h166bdaf_9 conda-forge libcblas 3.9.0 17_linux64_openblas conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libcurl 8.2.0 hca28451_0 conda-forge libdeflate 1.18 h0b41bf4_0 conda-forge libdrm 2.4.114 h166bdaf_0 conda-forge libedit 3.1.20221030 h5eee18b_0 libev 4.33 h516909a_1 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.4 h6a678d5_0 libgcc-ng 13.1.0 he5830b7_0 conda-forge libgfortran-ng 13.1.0 h69a702a_0 conda-forge libgfortran5 13.1.0 h15d22d2_0 conda-forge libgirepository 1.76.1 h8bf6c18_0 conda-forge libglib 2.76.4 hebfc3b9_0 conda-forge libgomp 13.1.0 he5830b7_0 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libidn2 2.3.4 h166bdaf_0 conda-forge libjpeg-turbo 2.1.5.1 h0b41bf4_0 conda-forge liblapack 3.9.0 17_linux64_openblas conda-forge libnghttp2 1.52.0 h61bc06f_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libopenblas 0.3.23 pthreads_h80387f5_0 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libpciaccess 0.17 h166bdaf_0 conda-forge libpng 1.6.39 h753d276_0 conda-forge librsvg 2.56.1 h98fae49_0 conda-forge libsqlite 3.42.0 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.1.0 hfd8a6a1_0 conda-forge libtasn1 4.19.0 h166bdaf_0 conda-forge libtiff 4.5.1 h8b53f26_0 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libva 2.19.0 hd590300_0 conda-forge libvpx 1.13.0 hcb278e6_0 conda-forge libwebp-base 1.3.1 hd590300_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxkbcommon 1.5.0 h5d7e998_3 conda-forge libxml2 2.11.4 h0d562d8_0 conda-forge libzlib 1.2.13 hd590300_5 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge mandrake 1.2.2 py38hd866c6d_2 conda-forge matplotlib-base 3.7.2 py38hf5b0b65_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge ncurses 6.4 hcb278e6_0 conda-forge nettle 3.8.1 hc379101_1 conda-forge networkx 3.1 pyhd8ed1ab_0 conda-forge numpy 1.24.4 py38h59b608b_0 conda-forge openblas 0.3.23 pthreads_h855a84d_0 conda-forge openh264 2.3.1 hcb278e6_2 conda-forge openjpeg 2.5.0 hfec8fc6_2 conda-forge openssl 3.1.1 hd590300_1 conda-forge p11-kit 0.24.1 hc5aa10d_0 conda-forge packaging 23.1 pyhd8ed1ab_0 conda-forge pandas 2.0.3 py38h01efb38_1 conda-forge pango 1.50.14 heaa33ce_1 conda-forge pcre2 10.40 hc3806b6_0 conda-forge pillow 10.0.0 py38h885162f_0 conda-forge pip 23.2 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge platformdirs 3.9.1 pyhd8ed1ab_0 conda-forge plotly 5.15.0 pyhd8ed1ab_0 conda-forge pooch 1.7.0 pyha770c72_3 conda-forge poppunk 2.6.0 py38hfd5d05e_1 bioconda pp-sketchlib 2.1.1 py38h1eec743_1 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pycairo 1.24.0 py38h1a1917b_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pygobject 3.44.1 py38hbbf0e52_0 conda-forge pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge pysocks 1.7.1 py38h578d9bd_5 conda-forge python 3.8.17 he550d4f_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.8 3_cp38 conda-forge pytz 2023.3 pyhd8ed1ab_0 conda-forge rapidnj 2.3.2 h4ac6f70_4 bioconda readline 8.2 h8228510_1 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge scikit-learn 1.3.0 py38hc099248_0 conda-forge scipy 1.10.1 py38h59b608b_3 conda-forge setuptools 68.0.0 pyhd8ed1ab_0 conda-forge sigcpp-3.0 3.4.0 hcb278e6_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sparsehash 2.0.4 hcb278e6_1 conda-forge svt-av1 1.6.0 h59595ed_0 conda-forge tenacity 8.2.2 pyhd8ed1ab_0 conda-forge threadpoolctl 3.2.0 pyha21a80b_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge tqdm 4.65.0 pyhd8ed1ab_1 conda-forge treeswift 1.1.37 pyh7cba7a3_0 bioconda typing-extensions 4.7.1 hd8ed1ab_0 conda-forge typing_extensions 4.7.1 pyha770c72_0 conda-forge unicodedata2 15.0.0 py38h0a891b7_0 conda-forge urllib3 2.0.4 pyhd8ed1ab_0 conda-forge wayland 1.22.0 h8c25dac_1 conda-forge wheel 0.40.0 pyhd8ed1ab_1 conda-forge x264 1!164.3095 h166bdaf_2 conda-forge x265 3.5 h924138e_3 conda-forge xkeyboard-config 2.39 hd590300_0 conda-forge xorg-compositeproto 0.4.2 h7f98852_1001 conda-forge xorg-damageproto 1.2.1 h7f98852_1002 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-inputproto 2.3.2 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.8.6 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxaw 1.0.14 h7f98852_1 conda-forge xorg-libxcomposite 0.4.6 h0b41bf4_1 conda-forge xorg-libxcursor 1.2.0 h0b41bf4_1 conda-forge xorg-libxdamage 1.1.5 h7f98852_1 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxi 1.7.10 h7f98852_0 conda-forge xorg-libxinerama 1.1.5 h27087fc_0 conda-forge xorg-libxmu 1.1.3 h7f98852_0 conda-forge xorg-libxpm 3.5.16 hd590300_0 conda-forge xorg-libxrandr 1.5.2 h7f98852_1 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-libxt 1.3.0 hd590300_0 conda-forge xorg-libxtst 1.2.3 h7f98852_1002 conda-forge xorg-randrproto 1.5.0 h7f98852_1001 conda-forge xorg-recordproto 1.14.2 h7f98852_1002 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-util-macros 1.19.3 h7f98852_0 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.4.2 h5eee18b_0 zipp 3.16.2 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstandard 0.19.0 py38h5945529_1 conda-forge zstd 1.5.5 hc292b87_0

[johnlees]

And can you also try running:

sketchlib --version

[hayleyjaywilson]

Hi John,

Apologies for the delay - cluster was down for maintenance!

sketchlib --version pp-sketchlib v2.1.1

Hayley

[johnlees]

Sorry for my delay too, just back from holiday

What is the result of running ls $CONDA_PREFIX/lib/python3.8/site-packages? Do you see files related to pp_sketchlib?

This is an odd one, I am guessing that the sketchlib library hasn't been installed where it's expected to be. I would suggest trying a new environment using python3.10 as a next step, but this may need a conda clearout. Another alternative could be to try the docker container on quay.io

[hayleyjaywilson]

Hi John,

output for you: ls $CONDA_PREFIX/lib/python3.8/site-packages Bio gi pip-23.2-py3.11.egg-info scikit_learn-1.3.0.dist-info biopython-1.81.dist-info graph_tool pkg_resources scipy BioSQL h5py platformdirs scipy-1.10.1.dist-info Brotli-1.0.9.dist-info h5py-3.8.0.dist-info platformdirs-3.9.1.dist-info setuptools _brotli.cpython-38-x86_64-linux-gnu.so hdbscan plotly setuptools-68.0.0-py3.11.egg-info brotli.py hdbscan-0.8.33.dist-info plotly-5.15.0.dist-info six-1.16.0.dist-info cached_property-1.5.2.dist-info idna _plotlyfuture six.py cached_property.py idna-3.4.dist-info _plotly_utils sklearn cairo importlib_resources pooch sockshandler.py certifi importlib_resources-6.0.0.dist-info pooch-1.7.0.dist-info socks.py certifi-2023.5.7-py3.11.egg-info joblib PopPUNK tenacity cffi joblib-1.3.0.dist-info poppunk-2.6.0.dist-info tenacity-8.2.2.dist-info cffi-1.15.1.dist-info jupyterlab_plotly poppunk_refine.cpython-38-x86_64-linux-gnu.so threadpoolctl-3.2.0.dist-info _cffi_backend.cpython-38-x86_64-linux-gnu.so kiwisolver pp_sketch threadpoolctl.py charset_normalizer kiwisolver-1.4.4.dist-info pp_sketchlib-2.1.1.dist-info tqdm charset_normalizer-3.2.0.dist-info mandrake pp_sketchlib.cpython-38-x86_64-linux-gnu.so tqdm-4.65.0.dist-info colorama mandrake-1.2.2.dist-info pycache treeswift colorama-0.4.6.dist-info matplotlib pycairo-1.24.0.egg-info treeswift-1.1.37.dist-info contourpy matplotlib-3.7.2.dist-info pycparser typing_extensions-4.7.1.dist-info contourpy-1.1.0.dist-info matplotlib-3.7.2-py3.8-nspkg.pth pycparser-2.21.dist-info typing_extensions.py cycler-0.11.0.dist-info mpl_toolkits PyGObject-3.44.1.egg-info tzdata cycler.py munkres-1.1.4-py3.6.egg-info pygtkcompat tzdata-2023.3.dist-info Cython munkres.py pylab.py unicodedata2-15.0.0.dist-info Cython-3.0.0.dist-info networkx pyparsing unicodedata2.cpython-38-x86_64-linux-gnu.so cython.py networkx-3.1.dist-info pyparsing-3.0.9.dist-info urllib3 dateutil numpy PySocks-1.7.1.dist-info urllib3-2.0.4.dist-info dendropy numpy-1.24.4.dist-info python_dateutil-2.8.2.dist-info wheel DendroPy-4.6.1.dist-info packaging pytz wheel-0.40.0.dist-info _distutils_hack packaging-23.1.dist-info pytz-2023.3.dist-info zipp distutils-precedence.pth pandas pyximport zipp-3.16.2.dist-info docopt-0.6.2-py2.7.egg-info pandas-2.0.3.dist-info README.txt zstandard docopt.py PIL requests zstandard-0.19.0-py3.8.egg-info fontTools Pillow-10.0.0.dist-info requests-2.31.0.dist-info fonttools-4.41.0.dist-info pip SCE.cpython-38-x86_64-linux-gnu.so

It looks like there are pp_sketchlib files there from what I can see. I will also try a new environment again and see what happens.

Thanks

---

From: John Lees @.> Sent: 14 August 2023 12:22 To: bacpop/PopPUNK @.> Cc: Hayley Joanna Wilson @.>; Author @.> Subject: Re: [bacpop/PopPUNK] Sketchlib back end not available? (Issue #278)

Sorry for my delay too, just back from holiday

What is the result of running ls $CONDA_PREFIX/lib/python3.8/site-packages? Do you see files related to pp_sketchlib?

This is an odd one, I am guessing that the sketchlib library hasn't been installed where it's expected to be. I would suggest trying a new environment using python3.10 as a next step, but this may need a conda clearout. Another alternative could be to try the docker container on quay.io

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