bacpop
poppunk_assign ERROR samples are missing from the final network
poppunk v2.4.0 conda list
packages in environment at /mnt/sdb/hc/soft/microGWAS/.snakemake/conda/ad4c981ca2c33d1b316d6ed40a3521b4_:
Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _x86_64-microarch-level 3 2_x86_64_v3 conda-forge apscheduler 3.11.0 pyh29332c3_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 h04ea711_2 conda-forge blinker 1.9.0 pyhff2d567_0 conda-forge brotli 1.1.0 hb03c661_4 conda-forge brotli-bin 1.1.0 hb03c661_4 conda-forge brotli-python 1.1.0 py310hea6c23e_4 conda-forge bzip2 1.0.8 hda65f42_8 conda-forge c-ares 1.34.5 hb9d3cd8_0 conda-forge ca-certificates 2025.10.5 hbd8a1cb_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.16.0 h44eff21_7 defaults cairomm-1.16 1.16.2 h7e731d7_1 conda-forge certifi 2025.10.5 pyhd8ed1ab_0 conda-forge cffi 2.0.0 py310h34a4b09_0 conda-forge charset-normalizer 3.4.3 pyhd8ed1ab_0 conda-forge click 8.3.0 pyh707e725_0 conda-forge colorama 0.4.6 pyhd8ed1ab_1 conda-forge contourpy 1.3.2 py310h3788b33_0 conda-forge cycler 0.12.1 pyhd8ed1ab_1 conda-forge dbus 1.13.6 h5008d03_3 conda-forge dendropy 5.0.8 pyhdfd78af_1 bioconda docopt 0.6.2 pyhd8ed1ab_2 conda-forge epoxy 1.5.10 hb03c661_2 conda-forge expat 2.7.1 hecca717_0 conda-forge flask 3.1.2 pyhd8ed1ab_0 conda-forge flask-apscheduler 1.13.1 pyhd8ed1ab_1 conda-forge flask-cors 6.0.1 pyhe01879c_0 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 h77eed37_3 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 4.60.1 py310h3406613_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge fribidi 1.0.16 hb03c661_0 conda-forge gdk-pixbuf 2.42.10 h5eee18b_1 defaults gettext 0.25.1 h3f43e3d_1 conda-forge gettext-tools 0.25.1 h3f43e3d_1 conda-forge glib 2.84.2 h6a678d5_0 defaults glib-tools 2.84.2 h6a678d5_0 defaults gmp 6.3.0 hac33072_2 conda-forge graph-tool 2.77 py310h0901348_300 conda-forge graph-tool-base 2.77 py310h9e900f9_300 conda-forge graphite2 1.3.14 hecca717_2 conda-forge gtk3 3.24.38 h280cfa0_1 conda-forge gunicorn 23.0.0 py310hff52083_2 conda-forge h2 4.3.0 pyhcf101f3_0 conda-forge h5py 3.13.0 nompi_py310h60e0fe6_100 conda-forge harfbuzz 8.2.1 h3d44ed6_0 conda-forge hdbscan 0.8.39 py310hf779ad0_1 conda-forge hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge hicolor-icon-theme 0.17 ha770c72_2 conda-forge hpack 4.1.0 pyhd8ed1ab_0 conda-forge hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.10 pyhd8ed1ab_1 conda-forge importlib-metadata 8.7.0 pyhe01879c_1 conda-forge itsdangerous 2.2.0 pyhd8ed1ab_1 conda-forge jinja2 3.1.6 pyhd8ed1ab_0 conda-forge joblib 1.5.2 pyhd8ed1ab_0 conda-forge jpeg 9e h0b41bf4_3 conda-forge keyutils 1.6.3 hb9d3cd8_0 conda-forge kiwisolver 1.4.9 py310haaf941d_1 conda-forge krb5 1.21.3 h659f571_0 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.44 ha97dd6f_2 conda-forge lerc 3.0 h9c3ff4c_0 conda-forge libaec 1.1.4 h3f801dc_0 conda-forge libasprintf 0.25.1 h3f43e3d_1 conda-forge libasprintf-devel 0.25.1 h3f43e3d_1 conda-forge libblas 3.9.0 36_h4a7cf45_openblas conda-forge libboost 1.84.0 hba137d9_3 conda-forge libboost-python 1.84.0 py310ha2bacc8_7 conda-forge libbrotlicommon 1.1.0 hb03c661_4 conda-forge libbrotlidec 1.1.0 hb03c661_4 conda-forge libbrotlienc 1.1.0 hb03c661_4 conda-forge libcblas 3.9.0 36_h0358290_openblas conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libcurl 8.8.0 hca28451_1 conda-forge libdeflate 1.10 h7f98852_0 conda-forge libdrm 2.4.125 hb03c661_1 conda-forge libedit 3.1.20250104 pl5321h7949ede_0 conda-forge libegl 1.7.0 ha4b6fd6_2 conda-forge libegl-devel 1.7.0 ha4b6fd6_2 conda-forge libev 4.33 hd590300_2 conda-forge libexpat 2.7.1 hecca717_0 conda-forge libffi 3.4.6 h2dba641_1 conda-forge libgcc 15.2.0 h767d61c_7 conda-forge libgcc-ng 15.2.0 h69a702a_7 conda-forge libgettextpo 0.25.1 h3f43e3d_1 conda-forge libgettextpo-devel 0.25.1 h3f43e3d_1 conda-forge libgfortran 15.2.0 h69a702a_7 conda-forge libgfortran-ng 15.2.0 h69a702a_7 conda-forge libgfortran5 15.2.0 hcd61629_7 conda-forge libgirepository 1.78.1 h003a4f0_1 conda-forge libgl 1.7.0 ha4b6fd6_2 conda-forge libgl-devel 1.7.0 ha4b6fd6_2 conda-forge libglib 2.84.2 h37c7471_0 defaults libglvnd 1.7.0 ha4b6fd6_2 conda-forge libglx 1.7.0 ha4b6fd6_2 conda-forge libglx-devel 1.7.0 ha4b6fd6_2 conda-forge libgomp 15.2.0 h767d61c_7 conda-forge libiconv 1.18 h3b78370_2 conda-forge liblapack 3.9.0 36_h47877c9_openblas conda-forge liblzma 5.8.1 hb9d3cd8_2 conda-forge liblzma-devel 5.8.1 hb9d3cd8_2 conda-forge libnghttp2 1.58.0 h47da74e_1 conda-forge libnsl 2.0.1 hb9d3cd8_1 conda-forge libopenblas 0.3.30 pthreads_h94d23a6_2 conda-forge libpciaccess 0.18 hb9d3cd8_0 conda-forge libpng 1.6.43 h2797004_0 conda-forge librsvg 2.56.3 h98fae49_0 conda-forge libsqlite 3.46.0 hde9e2c9_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx 15.2.0 h8f9b012_7 conda-forge libstdcxx-ng 15.2.0 h4852527_7 conda-forge libtiff 4.3.0 h0fcbabc_4 conda-forge libuuid 2.41.2 he9a06e4_0 conda-forge libwebp-base 1.6.0 hd42ef1d_0 conda-forge libxcb 1.17.0 h8a09558_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxkbcommon 1.7.0 h2c5496b_1 conda-forge libxml2 2.12.7 hc051c1a_1 conda-forge libzlib 1.2.13 h4ab18f5_6 conda-forge markupsafe 3.0.3 py310h3406613_0 conda-forge matplotlib-base 3.10.1 py310h68603db_0 conda-forge munkres 1.0.7 py_1 bioconda ncurses 6.5 h2d0b736_3 conda-forge networkx 3.4.2 pyh267e887_2 conda-forge numpy 2.2.6 py310hefbff90_0 conda-forge olefile 0.47 pyhd8ed1ab_1 conda-forge openblas 0.3.30 pthreads_h6ec200e_2 conda-forge openjpeg 2.5.0 h7d73246_0 conda-forge openssl 3.5.4 h26f9b46_0 conda-forge packaging 25.0 pyh29332c3_1 conda-forge pandas 2.3.3 py310h0158d43_1 conda-forge pango 1.50.14 ha41ecd1_2 conda-forge pcre2 10.42 hcad00b1_0 conda-forge pillow 8.4.0 py310h07f4688_0 conda-forge pip 25.2 pyh8b19718_0 conda-forge pixman 0.46.4 h54a6638_1 conda-forge poppunk 2.4.0 py310h2579afa_2 bioconda pp-sketchlib 2.1.3 py310h37665e0_0 conda-forge pthread-stubs 0.4 hb9d3cd8_1002 conda-forge pycairo 1.25.0 py310hda9f760_1 conda-forge pycparser 2.22 pyh29332c3_1 conda-forge pygobject 3.46.0 py310h30b043a_1 conda-forge pyparsing 3.2.5 pyhcf101f3_0 conda-forge pysocks 1.7.1 pyha55dd90_7 conda-forge python 3.10.14 hd12c33a_0_cpython conda-forge python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge python_abi 3.10 8_cp310 conda-forge pytz 2025.2 pyhd8ed1ab_0 conda-forge qhull 2020.2 h434a139_5 conda-forge rapidnj 2.3.2 h9948957_6 bioconda readline 8.2 h8c095d6_2 conda-forge requests 2.32.5 pyhd8ed1ab_0 conda-forge scikit-learn 1.7.2 py310h228f341_0 conda-forge scipy 1.15.2 py310h1d65ade_0 conda-forge setuptools 80.9.0 pyhff2d567_0 conda-forge sigcpp-3.0 3.6.0 h59595ed_0 conda-forge six 1.17.0 pyhe01879c_1 conda-forge sparsehash 2.0.2 0 bioconda threadpoolctl 3.6.0 pyhecae5ae_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tqdm 4.67.1 pyhd8ed1ab_1 conda-forge tzdata 2025b h78e105d_0 conda-forge tzlocal 5.3.1 pyh8f84b5b_0 conda-forge unicodedata2 16.0.0 py310h7c4b9e2_1 conda-forge urllib3 2.5.0 pyhd8ed1ab_0 conda-forge wayland 1.24.0 h3e06ad9_0 conda-forge werkzeug 3.1.3 pyhd8ed1ab_1 conda-forge wheel 0.45.1 pyhd8ed1ab_1 conda-forge xkeyboard-config 2.46 hb03c661_0 conda-forge xorg-libice 1.1.2 hb9d3cd8_0 conda-forge xorg-libsm 1.2.6 he73a12e_0 conda-forge xorg-libx11 1.8.12 h4f16b4b_0 conda-forge xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge xorg-libxaw 1.0.16 hb9d3cd8_0 conda-forge xorg-libxcomposite 0.4.6 hb9d3cd8_2 conda-forge xorg-libxcursor 1.2.3 hb9d3cd8_0 conda-forge xorg-libxdamage 1.1.6 hb9d3cd8_0 conda-forge xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge xorg-libxfixes 6.0.2 hb03c661_0 conda-forge xorg-libxi 1.8.2 hb9d3cd8_0 conda-forge xorg-libxinerama 1.1.5 h5888daf_1 conda-forge xorg-libxmu 1.2.1 hb9d3cd8_1 conda-forge xorg-libxpm 3.5.17 hb9d3cd8_1 conda-forge xorg-libxrandr 1.5.4 hb9d3cd8_0 conda-forge xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge xorg-libxxf86vm 1.1.6 hb9d3cd8_0 conda-forge xorg-xorgproto 2024.1 hb9d3cd8_1 conda-forge xz 5.8.1 hbcc6ac9_2 conda-forge xz-gpl-tools 5.8.1 hbcc6ac9_2 conda-forge xz-tools 5.8.1 hb9d3cd8_2 conda-forge zipp 3.23.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h4ab18f5_6 conda-forge zstandard 0.23.0 py310h7c4b9e2_3 conda-forge zstd 1.5.6 ha6fb4c9_0 conda-forge
poppunk_assign --db data/poppunk/pa/pa_pruned_threshold_005 --query out/poppunk_input.txt --output out/poppunk --threads 80
`/mnt/sdb/hc/soft/microGWAS/.snakemake/conda/ad4c981ca2c33d1b316d6ed40a3521b4_/lib/python3.10/site-packages/PopPUNK/unwords.py:5: 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. import pkg_resources PopPUNK: assign (with backend: sketchlib v2.1.4 sketchlib: /mnt/sdb/hc/soft/microGWAS/.snakemake/conda/ad4c981ca2c33d1b316d6ed40a3521b4_/lib/python3.10/site-packages/pp_sketchlib.cpython-310-x86_64-linux-gnu.so)
Graph-tools OpenMP parallelisation enabled: with 80 threads Mode: Assigning clusters of query sequences
Loading previously refined model Completed model loading Sketching 453 genomes using 80 thread(s) Progress (CPU): 453 / 453 Writing sketches to file WARNING: versions of input databases sketches are different, results may not be compatible Calculating distances using 80 thread(s) Progress (CPU): 100.0% Selected type isolate for distance QC is SAMD00019033 Network loaded: 6082 samples ERROR: 10 samples are missing from the final network `
See https://poppunk-docs.bacpop.org/troubleshooting.html#samples-are-missing-from-the-final-network
I used the complete Pseudomonas aeruginosa reference database from the site (https://www.bacpop.org/poppunk-databases/), but I am confused about the following statement: “Make sure the provided network is the one created by applying the --model-dir to --distances, and that the same output directory has not been used and overwritten by different steps or inputs.” I still don’t fully understand the specific steps. Could you please provide a more detailed explanation or example code? Thank you very much!
Sorry for the slow reply. Can you first please try upgrading poppunk to the most recent version (v2.7.6), v2.4.0 is over four years old
@johnlees I was still getting the same error, even after the software upgraded to v2.7.6.
Thanks for confirming. I can replicate this -- it's because our pseudomonas database is misformatted, sorry about that!
We will fix this on the website, but in the mean time you can get it to work if you rename the contents of the database directory pa_v1_full as follows:
pa_v1_full.dists.npy pa_v1_full_clusters.csv pa_v1_full_graph.gt
pa_v1_full.dists.pkl pa_v1_full_fit.npz pa_v1_full_refined_fit.png
pa_v1_full.h5 pa_v1_full_fit.pkl pa_v1_full_unword_clusters.csv
I did this by running:
rename 's/pa_pruned_threshold_005/pa_v1_full/' pa_v1_full/*
rename 's/pa_pruned_1sd/pa_v1_full/' pa_v1_full/*