search

nanoporetech / ont_fast5_api

Oxford Nanopore Technologies fast5 API software
Other
149 stars 29 forks source link

Issue while converting single_to_multi_fast5 #22

Closed andrese52 closed 5 years ago

andrese52 commented 5 years ago

I have a folder with thousands of single fast5s from a previous run. I want to convert them to fast5 containing 4k reads. I am running the following command:

module load python3
export HDF5_USE_FILE_LOCKING='FALSE'
single_to_multi_fast5 \
    --input_path fast5 \
    --save_path fast5_4000 \
    --threads 32 \
    --batch_size 4000 \
    --recursive

Although I have installed ont_fast5_api from the pip repository and later by cloning from here. The latest error that I am getting is:

/opt/anaconda3/5.1.0/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
ERROR:ont_fast5_api.conversion_tools.single_to_multi_fast5:'<' not supported between instances of 'str' and 'float'
        Failed to add single read file: 'fast5/FAK41369_973f0349d57554ff9d459dc3422546465b539a5f_814200.fast5' to 'fast5_4000_python3/batch_0.fast5'

The error is repeated many times as follows:

ERROR:ont_fast5_api.conversion_tools.single_to_multi_fast5:'<' not supported between instances of 'str' and 'float'
        Failed to add single read file: 'fast5/FAK41369_973f0349d57554ff9d459dc3422546465b539a5f_1601884.fast5' to 'fast5_4000_python3/batch_10.fast5'

May you please suggest a solution to this error?

Thank you

fbrennen commented 5 years ago

Hi @andrese52 -- could we have one of your fast5 files that's causing one of these errors?