Description
Hi,
I downloaded fast5 files for groups IVT and Vero-Infected (with corresponding fastaq files) from the repository: https://osf.io/8f6n9/. I run this code for fast5 files from the IVT group:
multi_to_single_fast5 -i IVT/fast5/ -s IVT/fast5_single/ -t 2
tombo preprocess annotate_raw_with_fastqs --fast5-basedir IVT/fast5_single/ --fastq-filenames IVT1.all.fastq
tombo resquiggle IVT/fast5_single/ covid.fasta --processes 4 --num-most-common-errors 5
And all goes smoothly. However, when I am trying to run the same for Vero-Infected group, tombo resquiggle command output is :
[22:30:48] Loading minimap2 reference. [22:30:48] Getting file list. [22:30:48] Loading default canonical ***** RNA ***** model. [22:30:48] Re-squiggling reads (raw signal to genomic sequence alignment). 5 most common unsuccessful read types (approx. %): ----- -----
64D5
----- ----- ----- 0%| | 0/8000 [00:00<?, ?it/s]Exception in thread Thread-1: Traceback (most recent call last): File "/usr/lib/python3.8/threading.py", line 932, in _bootstrap_inner self.run() File "/usr/lib/python3.8/threading.py", line 870, in run self._target(*self._args, **self._kwargs) File "/mnt/f/Chrome_Downloads/covid19/tombo/tombo/resquiggle.py", line 1662, in _io_and_mappy_thread_worker _io_and_map_read( File "/mnt/f/Chrome_Downloads/covid19/tombo/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/taras/.local/lib/python3.8/site-packages/h5py/_hl/dataset.py", line 573, in __getitem__ self.id.read(mspace, fspace, arr, mtype, dxpl=self._dxpl) 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/h5d.pyx", line 182, in h5py.h5d.DatasetID.read File "h5py/_proxy.pyx", line 130, in h5py._proxy.dset_rw File "h5py/_proxy.pyx", line 84, in h5py._proxy.H5PY_H5Dread OSError: Can't read data (can't open directory: /usr/local/hdf5/lib/plugin)
And the same for each thread. Progress bas stops on some number from 0 to 30 and stucks.
Is it some issue with fast5 files from Vero-Infected group or corresponding fastaq file?