Illegal instruction

[FKazuki0801]

I am interested in using funannotate2, but I am having trouble installing it with Conda on Linux.
When I type "funannotate2 -h," I receive an "illegal instruction" error.
I tried #4 , but got the same result.

Here is my machine information:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
Address sizes: 46 bits physical, 48 bits virtual
CPU(s): 32
On-line CPU(s) list: 0-31
Thread(s) per core: 1
Core(s) per socket: 8
Socket(s): 4
NUMA node(s): 4
Vendor ID: GenuineIntel
CPU family: 6
Model: 45
Model name: Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
Stepping: 7
CPU MHz: 2665.847
CPU max MHz: 2800.0000
CPU min MHz: 1200.0000
BogoMIPS: 4788.52
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 20480K
NUMA node0 CPU(s): 0-7
NUMA node1 CPU(s): 8-15
NUMA node2 CPU(s): 16-23
NUMA node3 CPU(s): 24-31
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx lahf_lm epb pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid xsaveopt dtherm ida arat pln pts md_clear flush_l1d

[nextgenusfs]

Sorry, I don't know how this would happen. I've installed on several linux systems as well as Mac. So unless you can come up with a reproducible example on docker or something, really impossible for me to address. It's just a python module, there is no underlying C libraries or anything else that would seemingly be the culprit.

[nextgenusfs]

Maybe one thing to try is just create a minimal conda python environment, and then install it from pip, ie

conda create -n test "python>=3.7,<3.13"
conda activate test
python -m pip install git+https://github.com/nextgenusfs/funannotate2.git

[FKazuki0801]

I create a docker image with this dockerfile

FROM amd64/ubuntu:latest

RUN apt-get update && \
    apt-get upgrade -y && \
    apt install -y wget git && \
    wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \
    bash Miniforge3-$(uname)-$(uname -m).sh -b && \
    /root/miniforge3/bin/conda init

and run this command:

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
conda config --remove channels default

First, I tried this:

conda create -n test "python>=3.7,<3.13"
conda activate test
python -m pip install git+https://github.com/nextgenusfs/funannotate2.git

This is the result:

(test) root@0646b134095d:/# python -m pip install git+https://github.com/nextgenusfs/funannotate2.git
Collecting git+https://github.com/nextgenusfs/funannotate2.git
  Cloning https://github.com/nextgenusfs/funannotate2.git to /tmp/pip-req-build-9wisnzls
  Running command git clone --filter=blob:none --quiet https://github.com/nextgenusfs/funannotate2.git /tmp/pip-req-build-9wisnzls
  Resolved https://github.com/nextgenusfs/funannotate2.git to commit 8b311468b6093ff526689d1c9d1e75142572a5f2
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting buscolite>=25.4.24 (from funannotate2==25.5.27)
  Using cached buscolite-25.4.24-py3-none-any.whl.metadata (6.5 kB)
Collecting gapmm2>=25.4.13 (from funannotate2==25.5.27)
  Using cached gapmm2-25.4.13-py3-none-any.whl.metadata (7.3 kB)
Collecting gb-io>=0.3.2 (from funannotate2==25.5.27)
  Using cached gb_io-0.3.6-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.8 kB)
Collecting gfftk>=24.10.29 (from funannotate2==25.5.27)
  Using cached gfftk-25.4.17-py3-none-any.whl.metadata (3.8 kB)
Collecting json-repair (from funannotate2==25.5.27)
  Using cached json_repair-0.46.0-py3-none-any.whl.metadata (12 kB)
Collecting mappy (from funannotate2==25.5.27)
  Using cached mappy-2.29.tar.gz (143 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting natsort (from funannotate2==25.5.27)
  Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting numpy (from funannotate2==25.5.27)
  Using cached numpy-2.2.6-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Collecting pyfastx>=2.0.0 (from funannotate2==25.5.27)
  Using cached pyfastx-2.2.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (30 kB)
Collecting pyhmmer>=0.10.15 (from funannotate2==25.5.27)
  Using cached pyhmmer-0.11.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (15 kB)
Collecting pytantan (from funannotate2==25.5.27)
  Using cached pytantan-0.1.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (50 kB)
Collecting requests (from funannotate2==25.5.27)
  Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting packaging (from buscolite>=25.4.24->funannotate2==25.5.27)
  Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Collecting edlib (from gapmm2>=25.4.13->funannotate2==25.5.27)
  Using cached edlib-1.3.9.post1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.1 kB)
Collecting psutil<8.0,>=6.0 (from pyhmmer>=0.10.15->funannotate2==25.5.27)
  Using cached psutil-7.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (22 kB)
Collecting archspec~=0.2 (from pytantan->funannotate2==25.5.27)
  Downloading archspec-0.2.5-py3-none-any.whl.metadata (4.4 kB)
Collecting scoring-matrices~=0.3.0 (from pytantan->funannotate2==25.5.27)
  Using cached scoring_matrices-0.3.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB)
Collecting charset-normalizer<4,>=2 (from requests->funannotate2==25.5.27)
  Downloading charset_normalizer-3.4.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB)
Collecting idna<4,>=2.5 (from requests->funannotate2==25.5.27)
  Downloading idna-3.10-py3-none-any.whl.metadata (10 kB)
Collecting urllib3<3,>=1.21.1 (from requests->funannotate2==25.5.27)
  Downloading urllib3-2.4.0-py3-none-any.whl.metadata (6.5 kB)
Collecting certifi>=2017.4.17 (from requests->funannotate2==25.5.27)
  Downloading certifi-2025.4.26-py3-none-any.whl.metadata (2.5 kB)
Using cached buscolite-25.4.24-py3-none-any.whl (144 kB)
Using cached gapmm2-25.4.13-py3-none-any.whl (19 kB)
Using cached gb_io-0.3.6-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (517 kB)
Using cached gfftk-25.4.17-py3-none-any.whl (4.7 MB)
Using cached pyfastx-2.2.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (841 kB)
Using cached pyhmmer-0.11.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.1 MB)
Using cached psutil-7.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (277 kB)
Using cached edlib-1.3.9.post1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (397 kB)
Using cached json_repair-0.46.0-py3-none-any.whl (22 kB)
Using cached natsort-8.4.0-py3-none-any.whl (38 kB)
Using cached numpy-2.2.6-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.5 MB)
Using cached packaging-25.0-py3-none-any.whl (66 kB)
Using cached pytantan-0.1.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (329 kB)
Downloading archspec-0.2.5-py3-none-any.whl (76 kB)
Using cached scoring_matrices-0.3.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (121 kB)
Downloading requests-2.32.3-py3-none-any.whl (64 kB)
Downloading charset_normalizer-3.4.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (148 kB)
Downloading idna-3.10-py3-none-any.whl (70 kB)
Downloading urllib3-2.4.0-py3-none-any.whl (128 kB)
Downloading certifi-2025.4.26-py3-none-any.whl (159 kB)
Building wheels for collected packages: funannotate2, mappy
  Building wheel for funannotate2 (pyproject.toml) ... done
  Created wheel for funannotate2: filename=funannotate2-25.5.27-py3-none-any.whl size=110906 sha256=491318afb73967be4d18f02176082929ca58ab0be5d38b72c819cccc0cfe7c3a
  Stored in directory: /tmp/pip-ephem-wheel-cache-34q0p0tu/wheels/f3/9c/ec/b9cbbccba3a81900e86d32796206e26fbb00ffcd409cddd3e1
  Building wheel for mappy (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Building wheel for mappy (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [23 lines of output]
      /tmp/pip-build-env-kbh7no58/overlay/lib/python3.12/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
      !!

              ********************************************************************************
              Please consider removing the following classifiers in favor of a SPDX license expression:

              License :: OSI Approved :: MIT License

              See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
              ********************************************************************************

      !!
        self._finalize_license_expression()
      running bdist_wheel
      running build
      running build_ext
      Compiling python/mappy.pyx because it changed.
      [1/1] Cythonizing python/mappy.pyx
      building 'mappy' extension
      creating build/temp.linux-x86_64-cpython-312
      creating build/temp.linux-x86_64-cpython-312/python
      gcc -pthread -B /root/miniforge3/envs/test/compiler_compat -fno-strict-overflow -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /root/miniforge3/envs/test/include -fPIC -O2 -isystem /root/miniforge3/envs/test/include -fPIC -I. -I/root/miniforge3/envs/test/include/python3.12 -c align.c -o build/temp.linux-x86_64-cpython-312/align.o -DHAVE_KALLOC -msse4.1
      error: command 'gcc' failed: No such file or directory
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for mappy
Successfully built funannotate2
Failed to build mappy
ERROR: Failed to build installable wheels for some pyproject.toml based projects (mappy)

Next, I tried the instrallation code:

mamba create -n funannotate2 gfftk gapmm2 minimap2 miniprot snap "augustus==3.5.0" glimmerhmm diamond trnascan-se table2asn gb-io buscolite
conda activate funannotate2
python -m pip install git+https://github.com/nextgenusfs/funannotate2.git
funannotate2 -h

This is the result:

(funannotate2) root@0646b134095d:/# funannotate2 -h
Illegal instruction

[nextgenusfs]

All of the tests here on github actions are using docker builds without issues. Not sure exactly what's wrong.

So mappy requires gcc I think to build, so need to add build-essential to the docker build.

But my point is that I don't think it's a funannotate2 issue you can add --no-deps to the pip command and id think that it should work.

[FKazuki0801]

Unfortunatery, I cannot solve this problem on conda environment. Sorry...

However, I am now able to run funannotate2 on venv environment via pip installation.

python -m venv funannotate2
source funannotate2/bin/activate
pip install git+https://github.com/nextgenusfs/funannotate2.git

Then,

❯ funannotate2 -h
usage: funannotate2 [-h] [--version] {install,clean,train,predict,annotate,species} ...

Funannotate: eukaryotic genome annotation pipeline

Commands:
  install     Install funannotate2 database files.
  clean       Find and remove duplicated contigs, sort by size, rename headers.
  train       Train ab intio gene prediction algorithms.
  predict     Predict primary gene models in a eukaryotic genome.
  annotate    Add functional annotation to gene models.
  species     View and manage species in F2 database.

Help:
  -h, --help  Show this help message and exit
  --version   show program's version number and exit

❯ funannotate2 --version
funannotate2 v25.5.27

Finally, I can tackle gene prediction analysis. Thanks!

[FKazuki0801]

Finally, I could solve the problem on comda environment. Thanks! (but, I don't know the reason...)