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weberlab-hhu / Helixer

Using Deep Learning to predict gene annotations
GNU General Public License v3.0
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using --write-by during export failing on at least some genomes #72

Closed alisandra closed 2 years ago

alisandra commented 2 years ago

Traceback (most recent call last): File "/home/ali/repos/github/weberlab-hhu/Helixer/export.py", line 71, in main(args) File "/home/ali/repos/github/weberlab-hhu/Helixer/export.py", line 25, in main controller.export(chunk_size=args.chunk_size, write_by=write_by, modes=modes, compression=args.compression, File "/home/ali/repos/github/weberlab-hhu/Helixer/helixer/export/exporter.py", line 223, in export for i, (flat_data, coord, masked_bases_perc, ig_bases_perc, h5_coord) in enumerate(numerify_outputs): File "/home/ali/repos/github/weberlab-hhu/Helixer/helixer/export/exporter.py", line 182, in _numerify_coord for coord_data, h5_coord in coord_data_gen: File "/home/ali/repos/github/weberlab-hhu/Helixer/helixer/export/numerify.py", line 368, in numerify for strand_res in CoordNumerifier._numerify_super_write_chunk(f_set, bp_coord, h5_coord, coord, max_len, File "/home/ali/repos/github/weberlab-hhu/Helixer/helixer/export/numerify.py", line 386, in _numerify_super_write_chunk xb = seq_numerifier.coord_to_matrices() File "/home/ali/repos/github/weberlab-hhu/Helixer/helixer/export/numerify.py", line 114, in coord_to_matrices self._zero_matrix() File "/home/ali/repos/github/weberlab-hhu/Helixer/helixer/export/numerify.py", line 92, in _zero_matrix self.matrix = np.zeros((self.length, self.n_cols,), self.dtype) ValueError: negative dimensions are not allowed

alisandra commented 2 years ago

fixed from 78313576c23eda96a1373614564cfc766978d11d