Array has an inhomogeneous shaper after 1 dimensions at features generation

[dacolombo]

Hi, when running the run_alphalink.sh script, I am getting this error in the MSA feature generation step, during the execution of the homo search:

I0509 20:49:32.189426 23456247969600 templates.py:777] hit 4clv_B did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.090625.
I0509 20:49:32.189463 23456247969600 templates.py:777] hit 5apq_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.078125.
I0509 20:49:32.189499 23456247969600 templates.py:777] hit 5apq_B did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.078125.
I0509 20:49:32.189536 23456247969600 templates.py:777] hit 5apq_C did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.078125.
I0509 20:49:32.189572 23456247969600 templates.py:777] hit 2n1t_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.065625.
I0509 20:49:32.189609 23456247969600 templates.py:777] hit 7dgx_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.04375.
I0509 20:49:32.189646 23456247969600 templates.py:777] hit 7dgx_B did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.04375.
I0509 20:49:32.189682 23456247969600 templates.py:777] hit 7d8r_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.0328125.
I0509 20:49:32.189718 23456247969600 templates.py:777] hit 7d8r_B did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.0328125.
I0509 20:49:32.189755 23456247969600 templates.py:777] hit 7d8r_C did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.0328125.
I0509 20:49:32.189791 23456247969600 templates.py:777] hit 7d8r_D did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.0328125.
I0509 20:49:32.189828 23456247969600 templates.py:777] hit 7qep_S6 did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.0484375.
fused_multi_tensor is not installed corrected
fused_layer_norm is not installed corrected
fused_softmax is not installed corrected
Traceback (most recent call last):
  File "/opt/AlphaLink2-1.1.1/unifold/homo_search.py", line 322, in <module>
    app.run(main)
  File "/opt/conda/envs/alphalink/lib/python3.10/site-packages/absl/app.py", line 308, in run
    _run_main(main, args)
  File "/opt/conda/envs/alphalink/lib/python3.10/site-packages/absl/app.py", line 254, in _run_main
    sys.exit(main(argv))
  File "/opt/AlphaLink2-1.1.1/unifold/homo_search.py", line 294, in main
    generate_pkl_features(
  File "/opt/AlphaLink2-1.1.1/unifold/homo_search.py", line 177, in generate_pkl_features
    feature_dict = data_pipeline.process(
  File "/opt/conda/envs/alphalink/lib/python3.10/site-packages/alphalink2-1.0-py3.10.egg/unifold/msa/pipeline.py", line 247, in process
    msa_features = make_msa_features((uniref90_msa, bfd_msa, mgnify_msa))
  File "/opt/conda/envs/alphalink/lib/python3.10/site-packages/alphalink2-1.0-py3.10.egg/unifold/msa/pipeline.py", line 81, in make_msa_features
    features["deletion_matrix_int"] = np.array(deletion_matrix, dtype=np.int32)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (3932,) + inhomogeneous part.

The same installation of AlphaLink2 works for other inputs and it seems to me that the input file used are correct. I tried looking at other AlphaFold and UniFold issues but couldn't find anything similar. What could be the cause of this issue?

[lhatsk]

Sorry, I have never seen this problem. Google suggests that downgrading NumPy helps sometimes...