Puumanamana / CoCoNet

Tool for unsupervised contig binning from viral metagenomes
Apache License 2.0
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coverage.h5 file missing #5

Open OlenaMaiakovska opened 1 year ago

OlenaMaiakovska commented 1 year ago

Dear authors, It seems there is coverage.h5 file missing in the output. What could be the reason?

Thank you in advance!

Best, Olena

coconet run --fasta ./contigs.fasta -bam ../*.bam --output binning_results_CoCoNet
11:24:09 (Mem:  0.5 GB)    <CoCoNet>    INFO: Using 5 threads
11:24:09 (Mem:  0.5 GB)    <CoCoNet>    INFO: Features: coverage, composition
11:24:09 (Mem:  0.5 GB) <preprocessing> INFO: Processing 4,455 contigs
11:24:09 (Mem:  0.5 GB) <preprocessing> INFO: Length filter (L>2048 bp) -> 10 contigs remaining
11:24:09 (Mem:  0.5 GB) <preprocessing> INFO: Complete contigs filtering (DTR > 10 bp) -> 10 contigs remaining
11:24:09 (Mem:  0.5 GB)   <learning>    INFO: Making train/test examples
11:24:09 (Mem:  0.5 GB)   <learning>    INFO: Parameters: fragment_step=128, fragment_length=1024, #training_samples=4000000, #test_samples=10000
Traceback (most recent call last):
  File "/home/olena/.local/bin/coconet", line 8, in <module>
    sys.exit(main())
  File "/home/olena/.local/lib/python3.8/site-packages/coconet/coconet.py", line 62, in main
    learn(cfg)
  File "/home/olena/.local/lib/python3.8/site-packages/coconet/coconet.py", line 197, in learn
    model = load_model(cfg)
  File "/home/olena/.local/lib/python3.8/site-packages/coconet/dl.py", line 67, in load_model
    input_shapes = config.get_input_shapes()
  File "/home/olena/.local/lib/python3.8/site-packages/coconet/core/config.py", line 198, in get_input_shapes
    with h5py.File(self.io['h5'], 'r') as handle:
  File "/home/olena/anaconda3/lib/python3.8/site-packages/h5py/_hl/files.py", line 567, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
  File "/home/olena/anaconda3/lib/python3.8/site-packages/h5py/_hl/files.py", line 231, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 106, in h5py.h5f.open
FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = '/home/olena/Projects/Metagenomic_Data/assembly/Virus_Discovery_for_Vietnam_Initiative_on_Zoonotic_Infections__VIZIONS_ERR3180356/Spades_output/binning_results_CoCoNet/coverage.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)