Getting JavaLang error on Ubuntu 22.04.5 LTS

[DeadlineWasYesterday]

I don't get the error on our CentOS 8.4.2105 system. I configure both environments to be as close as possible with conda. I tried with both Python versions 3.7 and 3.9 and Sepp versions 4.5.1 and 4.4.0. I tested pplacer on both machines and it works fine.

Here is the error message:

Here is the conda environment:

conda list output

# Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge bionick 0.0.4 pypi_0 pypi biopython 1.81 pypi_0 pypi blas 1.0 openblas anaconda bottleneck 1.3.5 py37h7deecbd_0 anaconda ca-certificates 2024.12.31 h06a4308_0 certifi 2022.12.7 py37h06a4308_0 compleasm 0.2.6 pyh7cba7a3_0 bioconda cycler 0.11.0 pypi_0 pypi dendropy 4.5.2 pyh3252c3a_0 bioconda fonttools 4.38.0 pypi_0 pypi hmmer 3.1b2 3 bioconda kiwisolver 1.4.5 pypi_0 pypi ld_impl_linux-64 2.40 h12ee557_0 libffi 3.4.4 h6a678d5_1 libgcc 14.2.0 h77fa898_1 conda-forge libgcc-ng 14.2.0 h69a702a_1 conda-forge libgfortran-ng 11.2.0 h00389a5_1 anaconda libgfortran5 11.2.0 h1234567_1 anaconda libgomp 14.2.0 h77fa898_1 conda-forge libnsl 2.0.0 h5eee18b_0 anaconda libopenblas 0.3.21 h043d6bf_0 anaconda libsqlite 3.45.2 h2797004_0 conda-forge libstdcxx-ng 11.2.0 h1234567_1 libzlib 1.3.1 hb9d3cd8_2 conda-forge matplotlib 3.5.3 pypi_0 pypi miniprot 0.13 h577a1d6_2 bioconda ncurses 6.4 h6a678d5_0 numexpr 2.8.4 py37hd2a5715_0 anaconda numpy 1.21.5 py37hf838250_3 anaconda numpy-base 1.21.5 py37h1e6e340_3 anaconda openjdk 8.0.152 h7b6447c_3 anaconda openssl 3.0.15 h5eee18b_0 anaconda packaging 22.0 py37h06a4308_0 anaconda pandas 1.3.5 py37h8c16a72_0 anaconda pillow 9.5.0 pypi_0 pypi pip 22.3.1 py37h06a4308_0 pplacer 1.1.alpha19 h9ee0642_2 bioconda pyparsing 3.1.4 pypi_0 pypi python 3.7.12 hf930737_100_cpython conda-forge python-dateutil 2.8.2 pyhd3eb1b0_0 anaconda python_abi 3.7 4_cp37m conda-forge pytz 2022.7 py37h06a4308_0 anaconda readline 8.2 h5eee18b_0 scipy 1.7.3 pypi_0 pypi seaborn 0.12.2 pypi_0 pypi sepp 4.5.1 py37he4bd417_1 bioconda setuptools 65.6.3 py37h06a4308_0 six 1.16.0 pyhd3eb1b0_1 anaconda sqlite 3.45.2 h2c6b66d_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge typing-extensions 4.7.1 pypi_0 pypi uniphy 0.0.1 pypi_0 pypi wheel 0.38.4 py37h06a4308_0 xz 5.4.6 h5eee18b_1 zlib 1.3.1 hb9d3cd8_2 conda-forge

[DeadlineWasYesterday]

Update: I was able to fix the issue from the pull request: #138 .

I replaced the original binary jar file with @sjanssen2 's one and it seems to be working.