PengNi
commented
2 years ago Hi @HeLi-80 , it seems the plugin wasn't imported correctly, Tombo still had to find plugin in /usr/lib/x86_64-linux-gnu/hdf5/serial/plugins.
What was the command you used to export the path of the vbz-plugin?
Best, Peng
HeLi-80
Hi, I'm having trouble with tombo resquiggle using my fast5s. Everything is fine up to tombo preprocess, but then tombo resquiggle crashes. I added ont-vbz-hdf-plugin to my environment but nothing changed. Here is the result of tombo resquiggle:
[17:39:37] Loading minimap2 reference. [17:39:55] Getting file list. [17:39:55] Loading default canonical DNA model. [17:39:55] Re-squiggling reads (raw signal to genomic sequence alignment). 0%| | 0/10 [00:00<?, ?it/s]Exception in thread Thread-1 (_io_and_mappy_thread_worker): Traceback (most recent call last): File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner self.run() File "/usr/lib/python3.10/threading.py", line 953, in run self._target(*self._args, self._kwargs) File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1662, in _io_and_mappy_thread_worker _io_and_map_read( File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1395, in _io_and_map_read all_raw_signal = th.get_raw_read_slot(fast5_data)['Signal'][:] File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/dataset.py", line 710, in getitem return self._fast_reader.read(args) File "h5py/_debian_h5py_serial/_selector.pyx", line 366, in h5py._debian_h5py_serial._selector.Reader.read OSError: Can't read data (can't open directory: /usr/lib/x86_64-linux-gnu/hdf5/serial/plugins) Exception in thread Thread-3 (_io_and_mappy_thread_worker): Traceback (most recent call last): File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner self.run() File "/usr/lib/python3.10/threading.py", line 953, in run Exception in thread Thread-5 (_io_and_mappy_thread_worker): Traceback (most recent call last): File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner self._target(*self._args, *self._kwargs) File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1662, in _io_and_mappy_thread_worker self.run() File "/usr/lib/python3.10/threading.py", line 953, in run _io_and_map_read( File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1395, in _io_and_map_read self._target(self._args, self._kwargs) all_raw_signal = th.get_raw_read_slot(fast5_data)['Signal'][:] File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1662, in _io_and_mappy_thread_worker _io_and_map_read( File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1395, in _io_and_map_read File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in h5py._debian_h5py_serial._objects.with_phil.wrapper all_raw_signal = th.get_raw_read_slot(fast5_data)['Signal'][:] File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/dataset.py", line 710, in getitem File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in h5py._debian_h5py_serial._objects.with_phil.wrapper return self._fast_reader.read(args) File "h5py/_debian_h5py_serial/_selector.pyx", line 366, in h5py._debian_h5py_serial._selector.Reader.read File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/dataset.py", line 710, in getitem OSError: Can't read data (can't open directory: /usr/lib/x86_64-linux-gnu/hdf5/serial/plugins) return self._fast_reader.read(args) File "h5py/_debian_h5py_serial/_selector.pyx", line 366, in h5py._debian_h5py_serial._selector.Reader.read OSError: Can't read data (can't open directory: /usr/lib/x86_64-linux-gnu/hdf5/serial/plugins) Exception in thread Thread-7 (_io_and_mappy_thread_worker): Traceback (most recent call last): File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner self.run() File "/usr/lib/python3.10/threading.py", line 953, in run self._target(*self._args, self._kwargs) File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1662, in _io_and_mappy_thread_worker _io_and_map_read( File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1395, in _io_and_map_read all_raw_signal = th.get_raw_read_slot(fast5_data)['Signal'][:] File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/dataset.py", line 710, in getitem return self._fast_reader.read(args) File "h5py/_debian_h5py_serial/_selector.pyx", line 366, in h5py._debian_h5py_serial._selector.Reader.read OSError: Can't read data (can't open directory: /usr/lib/x86_64-linux-gnu/hdf5/serial/plugins) Exception in thread Thread-8 (_io_and_mappy_thread_worker): Traceback (most recent call last): File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner self.run() File "/usr/lib/python3.10/threading.py", line 953, in run self._target(*self._args, *self._kwargs) File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1662, in _io_and_mappy_thread_worker _io_and_map_read( File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1395, in _io_and_map_read all_raw_signal = th.get_raw_read_slot(fast5_data)['Signal'][:] File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/dataset.py", line 710, in getitem return self._fast_reader.read(args) File "h5py/_debian_h5py_serial/_selector.pyx", line 366, in h5py._debian_h5py_serial._selector.Reader.read OSError: Can't read data (can't open directory: /usr/lib/x86_64-linux-gnu/hdf5/serial/plugins) Exception in thread Thread-10 (_io_and_mappy_thread_worker): Traceback (most recent call last): File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner self.run() File "/usr/lib/python3.10/threading.py", line 953, in run self._target(self._args, self._kwargs) File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1662, in _io_and_mappy_thread_worker _io_and_map_read( File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1395, in _io_and_map_read all_raw_signal = th.get_raw_read_slot(fast5_data)['Signal'][:] File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in h5py._debian_h5py_serial._objects.with_phil.wrapper Exception in thread Thread-9 (_io_and_mappy_thread_worker): Traceback (most recent call last): File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner self.run() File "/usr/lib/python3.10/threading.py", line 953, in run File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/dataset.py", line 710, in getitem self._target(*self._args, self._kwargs) return self._fast_reader.read(args) File "h5py/_debian_h5py_serial/_selector.pyx", line 366, in h5py._debian_h5py_serial._selector.Reader.read File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1662, in _io_and_mappy_thread_worker OSError: Can't read data (can't open directory: /usr/lib/x86_64-linux-gnu/hdf5/serial/plugins) _io_and_map_read( File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1395, in _io_and_map_read all_raw_signal = th.get_raw_read_slot(fast5_data)['Signal'][:] File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/dataset.py", line 710, in getitem return self._fast_reader.read(args) File "h5py/_debian_h5py_serial/_selector.pyx", line 366, in h5py._debian_h5py_serial._selector.Reader.read OSError: Can't read data (can't open directory: /usr/lib/x86_64-linux-gnu/hdf5/serial/plugins) Exception in thread Thread-2 (_io_and_mappy_thread_worker): Traceback (most recent call last): File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner self.run() File "/usr/lib/python3.10/threading.py", line 953, in run self._target(*self._args, *self._kwargs) File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1662, in _io_and_mappy_thread_worker _io_and_map_read( File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1395, in _io_and_map_read all_raw_signal = th.get_raw_read_slot(fast5_data)['Signal'][:] File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in h5py._debian_h5py_serial._objects.with_phil.wrapper Exception in thread Thread-4 (_io_and_mappy_thread_worker): Traceback (most recent call last): File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in h5py._debian_h5py_serial._objects.with_phil.wrapper self.run() File "/usr/lib/python3.10/threading.py", line 953, in run File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/dataset.py", line 710, in getitem self._target(self._args, self._kwargs) File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1662, in _io_and_mappy_thread_worker return self._fast_reader.read(args) _io_and_map_read( File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1395, in _io_and_map_read File "h5py/_debian_h5py_serial/_selector.pyx", line 366, in h5py._debian_h5py_serial._selector.Reader.read Exception in thread Thread-6 (_io_and_mappy_thread_worker): all_raw_signal = th.get_raw_read_slot(fast5_data)['Signal'][:] File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in h5py._debian_h5py_serial._objects.with_phil.wrapper OSError: Can't read data (can't open directory: /usr/lib/x86_64-linux-gnu/hdf5/serial/plugins) Traceback (most recent call last): File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner self.run() File "/usr/lib/python3.10/threading.py", line 953, in run File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/dataset.py", line 710, in getitem self._target(*self._args, **self._kwargs) File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1662, in _io_and_mappy_thread_worker return self._fast_reader.read(args) File "h5py/_debian_h5py_serial/_selector.pyx", line 366, in h5py._debian_h5py_serial._selector.Reader.read _io_and_map_read( File "/usr/lib/python3/dist-packages/tombo/resquiggle.py", line 1395, in _io_and_map_read OSError: Can't read data (can't open directory: /usr/lib/x86_64-linux-gnu/hdf5/serial/plugins) all_raw_signal = th.get_raw_read_slot(fast5_data)['Signal'][:] File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in h5py._debian_h5py_serial._objects.with_phil.wrapper File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/dataset.py", line 710, in getitem return self._fast_reader.read(args) File "h5py/_debian_h5py_serial/_selector.pyx", line 366, in h5py._debian_h5py_serial._selector.Reader.read OSError: Can't read data (can't open directory: /usr/lib/x86_64-linux-gnu/hdf5/serial/plugins)
Thank you