Numpy issue in hapdup 0.12 singularity image

[Alxdu]

Using the singularity image created from the official docker for hapdup 0.12, getting this error. Appears to be related to a deprecated numpy function while running pepper.

apptainer exec ../hapdup_0.12.sif  hapdup --assembly assembly.fasta --bam lr_mapping.bam --out-dir hapdup -t 48 --rtype ont
[2025-07-03 12:48:42] INFO: Filtering alignments
[2025-07-03 12:50:03] INFO: Running: flye-samtools index -@4 hapdup/filtered.bam
[2025-07-03 12:50:10] INFO: Running: pepper_variant call_variant -b /storage/LOKISHARED/yeast_assembly_nextflow_2025/test_hapdup/hapdup/filtered.bam -f /storage/LOKISHARED/yeast_assembly_nextflow_2025/test_hapdup/assembly.fasta -o /storage/LOKISHARED/yeast_assembly_nextflow_2025/test_hapdup/hapdup/pepper -m hapdup/pepper/pepper_model.bin -t 48 -s Sample --ont_r9_guppy5_sup --include-supplementary --no_quantized 2>&1 |tee hapdup/pepper/pepper.log
Traceback (most recent call last):
  File "/usr/local/bin/pepper_variant", line 5, in <module>
    from pepper_variant.pepper_variant import main
  File "/usr/local/lib/python3.8/dist-packages/pepper_variant/pepper_variant.py", line 11, in <module>
    from pepper_variant.modules.python.ImageGenerationUI import ImageGenerationUtils
  File "/usr/local/lib/python3.8/dist-packages/pepper_variant/modules/python/ImageGenerationUI.py", line 12, in <module>
    from pepper_variant.modules.python.DataStore import DataStore
  File "/usr/local/lib/python3.8/dist-packages/pepper_variant/modules/python/DataStore.py", line 1, in <module>
    import h5py
  File "/usr/local/lib/python3.8/dist-packages/h5py/__init__.py", line 46, in <module>
    from ._conv import register_converters as _register_converters
  File "h5py/h5t.pxd", line 14, in init h5py._conv
  File "h5py/h5t.pyx", line 293, in init h5py.h5t
  File "/home/axd/.local/lib/python3.8/site-packages/numpy/__init__.py", line 320, in __getattr__
    raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'typeDict'
rm: cannot remove 'hapdup/pepper/images*': No such file or directory
rm: cannot remove 'hapdup/pepper/predictions*': No such file or directory
[2025-07-03 12:50:10] ERROR: Missing output: /storage/LOKISHARED/yeast_assembly_nextflow_2025/test_hapdup/hapdup/pepper/PEPPER_VARIANT_FULL.vcf
Traceback (most recent call last):
  File "/usr/local/bin/hapdup", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.8/dist-packages/hapdup/main.py", line 190, in main
    file_check(pepper_vcf)
  File "/usr/local/lib/python3.8/dist-packages/hapdup/main.py", line 114, in file_check
    raise Exception("Missing output")
Exception: Missing output

[mikolmogorov]

Very strange, seems like exactly the scenario Docker was designed to solve.. Does it work if you run it via docker run? Or via singularity? Never seen this before, and the docker image has not been updated recently.