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haotianteng / Chiron

A basecaller for Oxford Nanopore Technologies' sequencers
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training data preparation #92

Closed WenxuZhang closed 5 years ago

WenxuZhang commented 5 years ago

Hi,

I am trying to train a new model. When I am prepare the training data, I get the error:

:~/Documents/nanopore/demo/test$ chiron export -i trash -o output ('model_default_path', '/usr/local/lib/python2.7/dist-packages/chiron/model/DNA_default') /home/wenxu/.local/lib/python2.7/site-packages/h5py/_hl/dataset.py:313: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. "Use dataset[()] instead.", H5pyDeprecationWarning) 'read_start_rel_to_raw' FAIL on trash/DEAMERNANOPORE_20161117_FNFAB43577_MN16450_sequencing_run_MA_821_R9_4_NA12878_11_17_16_88738_ch16_read937_strand.fast5 file.

Could you help on that?

haotianteng commented 5 years ago

For training purpose, the reads have to be labeled first using software like Tombo. Please refer to the training section on Chiron README.md