Using simple remapping fails

[sacdallago]

You can check out /mnt/project/bio_embeddings/runs/cath on rostssh.

stderr.log there will tell you:

Traceback (most recent call last):
  File "/mnt/lsf-nas-1/os-shared/anaconda3/envs/bio_embeddings_unstable/bin/bio_embeddings", line 8, in <module>
    sys.exit(main())
  File "/mnt/lsf-nas-1/os-shared/anaconda3/envs/bio_embeddings_unstable/lib/python3.8/site-packages/bio_embeddings/utilities/cli.py", line 22, in main
    run(arguments.config_path[0], overwrite=arguments.overwrite)
  File "/mnt/lsf-nas-1/os-shared/anaconda3/envs/bio_embeddings_unstable/lib/python3.8/site-packages/bio_embeddings/utilities/pipeline.py", line 166, in run
    stage_output_parameters = stage_runnable(**stage_parameters)
  File "/mnt/lsf-nas-1/os-shared/anaconda3/envs/bio_embeddings_unstable/lib/python3.8/site-packages/bio_embeddings/embed/pipeline.py", line 276, in run
    return PROTOCOLS[kwargs["protocol"]](**kwargs)
  File "/mnt/lsf-nas-1/os-shared/anaconda3/envs/bio_embeddings_unstable/lib/python3.8/site-packages/bio_embeddings/embed/pipeline.py", line 196, in seqvec
    return embed_and_write_batched(embedder, file_manager, result_kwargs)
  File "/mnt/lsf-nas-1/os-shared/anaconda3/envs/bio_embeddings_unstable/lib/python3.8/site-packages/bio_embeddings/embed/pipeline.py", line 166, in embed_and_write_batched
    reduced_embeddings_file.create_dataset(
  File "/mnt/lsf-nas-1/os-shared/anaconda3/envs/bio_embeddings_unstable/lib/python3.8/site-packages/h5py/_hl/group.py", line 139, in create_dataset
    self[name] = dset
  File "/mnt/lsf-nas-1/os-shared/anaconda3/envs/bio_embeddings_unstable/lib/python3.8/site-packages/h5py/_hl/group.py", line 370, in __setitem__
    name, lcpl = self._e(name, lcpl=True)
  File "/mnt/lsf-nas-1/os-shared/anaconda3/envs/bio_embeddings_unstable/lib/python3.8/site-packages/h5py/_hl/base.py", line 137, in _e
    name = name.encode('ascii')
AttributeError: 'int' object has no attribute 'encode'

You probably have to cast the int to str when saving the embedding. I remember I fixed this in the past, but probably due to significant overwrites, it got lost...

Please, once you fixed this issue, can you try re-running the job?

Instructions in: /mnt/project/bio_embeddings/README