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nanoporetech / tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
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tombo resquiggle error #383

Open wentski opened 2 years ago

wentski commented 2 years ago

Hello,

I am having trouble running tombo resquiggle on my samples. I have tried running the command both for samples which were basecalled during the sequencing run on MinKnow and for samples which were basecalled post-sequencing using guppy. Both methods give the same error. I have even tried removing basecalling tags using ont-fast5-api's --sanitize option and rebasecalling but get the same result:

Exception in thread Thread-8: Traceback (most recent call last): File "/home/sxtm38/miniconda3/lib/python3.7/threading.py", line 926, in _bootstrap_inner self.run() File "/home/sxtm38/miniconda3/lib/python3.7/threading.py", line 870, in run self._target(*self._args, **self._kwargs) File "/home/sxtm38/miniconda3/lib/python3.7/site-packages/tombo/resquiggle.py", line 1667, in _io_and_mappy_thread_worker sig_len_rng, seq_len_rng) File "/home/sxtm38/miniconda3/lib/python3.7/site-packages/tombo/resquiggle.py", line 1395, in _io_and_map_read all_raw_signal = th.get_raw_read_slot(fast5_data)['Signal'][:] 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 "/home/sxtm38/miniconda3/lib/python3.7/site-packages/h5py/_hl/dataset.py", line 710, in getitem return self._fast_reader.read(args) File "h5py/_selector.pyx", line 366, in h5py._selector.Reader.read OSError: Can't read data (can't open directory: /home/sxtm38/miniconda3/lib/hdf5/plugin)

Strangely, running the same command on older files works fine. Is there perhaps an incompatibility with certain guppy versions? I am really not sure what to make of this. Any help appreciated.

AnWiercze commented 2 years ago

Same issue!

marcus1487 commented 2 years ago

This looks like an issue with the VBZ compression. Can you try the suggestion here https://github.com/nanoporetech/tombo/issues/268#issuecomment-658704895

AnWiercze commented 2 years ago

In my case, the HDF5_PLUGIN_PATH is already exported and stored in the bashrc.

AnWiercze commented 2 years ago

Could solve the issue by installing the ont-vbz plugin via anaconda and python 3.6: conda install -c bioconda ont_vbz_hdf_plugin

wentski commented 2 years ago

Issue solved. I downloaded the ont-vbz plugin and placed a copy in the miniconda3/lib/hdf5/plugin folder. Thanks for the suggestions.