Error when running --call

[vealvarez]

Hello everyone!

I am getting this error when trying to run --call:

Could you please help me?

Thanks

[johnlees]

How have you installed unitig-caller, and what versions of bifrost do you have installed? If you could provide the output of conda list or similar, that would be very helpful.

Also if possible please post output as text rather than a screenshot (you can enclose in triple backticks ``` to format correctly) -- this makes it easier for us to search using the error messages!

[vealvarez]

I have installed unitig-caller with conda: conda install unitig-caller

I haven't installed bifrost. How do I install it?

This is conda list:

packages in environment at /home/vero/Documentos/Programas/mambaforge:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge bifrost 1.3.1 h43eeafb_0 bioconda boltons 23.0.0 pyhd8ed1ab_0 conda-forge brotli-python 1.1.0 py310hc6cd4ac_0 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.19.1 hd590300_0 conda-forge ca-certificates 2023.11.17 hbcca054_0 conda-forge certifi 2023.11.17 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py310h255011f_3 conda-forge charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge conda 23.3.1 py310hff52083_0 conda-forge conda-libmamba-solver 23.3.0 pyhd8ed1ab_0 conda-forge conda-package-handling 2.2.0 pyh38be061_0 conda-forge conda-package-streaming 0.9.0 pyhd8ed1ab_0 conda-forge cryptography 41.0.3 py310h75e40e8_0 conda-forge fmt 9.1.0 h924138e_0 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge jsonpatch 1.32 pyhd8ed1ab_0 conda-forge jsonpointer 2.0 py_0 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.21.2 h659d440_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge libarchive 3.6.2 h039dbb9_1 conda-forge libcurl 8.2.1 hca28451_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.1.0 he5830b7_0 conda-forge libgomp 13.1.0 he5830b7_0 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libmamba 1.4.2 hcea66bb_0 conda-forge libmambapy 1.4.2 py310h1428755_0 conda-forge libnghttp2 1.52.0 h61bc06f_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libsolv 0.7.24 hfc55251_3 conda-forge libsqlite 3.43.0 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.1.0 hfd8a6a1_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libxml2 2.11.5 h232c23b_1 conda-forge libzlib 1.2.13 hd590300_5 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge lzo 2.10 h516909a_1000 conda-forge mamba 1.4.2 py310h51d5547_0 conda-forge ncurses 6.4 hcb278e6_0 conda-forge openssl 3.2.0 hd590300_1 conda-forge packaging 23.1 pyhd8ed1ab_0 conda-forge pip 23.2.1 pyhd8ed1ab_0 conda-forge pluggy 1.3.0 pyhd8ed1ab_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pybind11-abi 4 hd8ed1ab_3 conda-forge pycosat 0.6.4 py310h5764c6d_1 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge python 3.10.12 hd12c33a_0_cpython conda-forge python_abi 3.10 3_cp310 conda-forge readline 8.2 h8228510_1 conda-forge reproc 14.2.4 h0b41bf4_0 conda-forge reproc-cpp 14.2.4 hcb278e6_0 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge ruamel.yaml 0.17.32 py310h2372a71_0 conda-forge ruamel.yaml.clib 0.2.7 py310h1fa729e_1 conda-forge setuptools 68.1.2 pyhd8ed1ab_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge tqdm 4.66.1 pyhd8ed1ab_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge unitig-caller 1.3.0 py310ha320341_2 bioconda urllib3 2.0.4 pyhd8ed1ab_0 conda-forge wheel 0.41.2 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml-cpp 0.7.0 h27087fc_2 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstandard 0.19.0 py

[johnlees]

Great, thanks. Could you also please paste as text the original error message you got?

@samhorsfield96 any known incompatibility issue w/ bifrost 1.3.1 and unitig-caller? I can see that 1.3.1 was released a couple of months ago. Might just be that we need a rebuild with the new library.

Function missing is BlockedBloomFilter::ReadBloomFilter(_IO_FILE*)

[johnlees]

I don't see anything in the release notes about that function changing, but seems like 1.3.0 isn't backwards compatible with older .bfi files

[vealvarez]

Great, thanks. Could you also please paste as text the original error message you got?

@samhorsfield96 any known incompatibility issue w/ bifrost 1.3.1 and unitig-caller? I can see that 1.3.1 was released a couple of months ago. Might just be that we need a rebuild with the new library

Traceback (most recent call last):
  File "/home/vero/Documentos/Programas/mambaforge/bin/unitig-caller", line 7, in <module>
    from unitig_caller.__main__ import main
  File "/home/vero/Documentos/Programas/mambaforge/lib/python3.10/site-packages/unitig_caller/__main__.py", line 11, in <module>
    import unitig_query
ImportError: /home/vero/Documentos/Programas/mambaforge/lib/python3.10/site-packages/unitig_query.cpython-310-x86_64-linux-gnu.so: undefined symbol: _ZN18BlockedBloomFilter15ReadBloomFilterEP8_IO_FILE

[johnlees]

Doing a rebuild here: https://github.com/bioconda/bioconda-recipes/pull/45035

[vealvarez]

Thanks! Will this version be available through bioconda?

[johnlees]

Yes, when it's merged I can give you instructions on how to update.

For now, I think if you reinstall and downgrade bifrost with conda install bifrost==1.2.0 it should work

[vealvarez]

Ok, I prefer to wait for instructions on how to update unitig-caller

[johnlees]

The fixed version is now on conda. Try reinstalling, it would be easiest if you used the same command to make a new environment entirely. Make sure you have build 3, you'll see the line unitig-caller 1.3.0 py310ha320341_3 bioconda in your conda list if this was resolved correctly (above you have build 2)