Hi,
I'm running poreplex in a linux machine using the following command:
poreplex -i /home3/Data/Nanopore/DIRECT_RNA/run_250319_Wt/fast5_pass/
-o /home/epicardi/Nanopore/pass --trim-adapter --parallel 20 --align /home/epicardi/minimap2index/mm10.mmi --fastq
For each running process I'm getting:
2019-04-02 13:48:03,498 [signal_analyzer.py:114] (FAK29499_e03ca1e3175e68134af1625d2dc20000581e13e5_0.fast5#94610be8-25e4-4a12-980b-2376634ebfe7) Unha
ndled exception KeyError: "Can't open attribute (can't locate attribute: 'num_events_template')"
Traceback (most recent call last):
File "/home/epicardi/bin/miniconda2/envs/py3/lib/python3.6/site-packages/poreplex/signal_analyzer.py", line 114, in process
siganal.process()
File "/home/epicardi/bin/miniconda2/envs/py3/lib/python3.6/site-packages/poreplex/signal_analyzer.py", line 259, in process
events = self.load_events()
File "/home/epicardi/bin/miniconda2/envs/py3/lib/python3.6/site-packages/poreplex/signal_analyzer.py", line 315, in load_events
events = self.npread.load_fast5_events()
File "/home/epicardi/bin/miniconda2/envs/py3/lib/python3.6/site-packages/poreplex/signal_loader.py", line 265, in load_fast5_events
bcall = self.fast5.get_basecall()
File "/home/epicardi/bin/miniconda2/envs/py3/lib/python3.6/site-packages/poreplex/fast5_file.py", line 142, in get_basecall
summary['num_events'] = int(segattrs['num_events_template'])
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/epicardi/bin/miniconda2/envs/py3/lib/python3.6/site-packages/h5py/_hl/attrs.py", line 60, in getitem
attr = h5a.open(self._id, self._e(name))
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/h5a.pyx", line 77, in h5py.h5a.open
KeyError: "Can't open attribute (can't locate attribute: 'num_events_template')"
Hi, I'm running poreplex in a linux machine using the following command: poreplex -i /home3/Data/Nanopore/DIRECT_RNA/run_250319_Wt/fast5_pass/ -o /home/epicardi/Nanopore/pass --trim-adapter --parallel 20 --align /home/epicardi/minimap2index/mm10.mmi --fastq
For each running process I'm getting:
2019-04-02 13:48:03,498 [signal_analyzer.py:114] (FAK29499_e03ca1e3175e68134af1625d2dc20000581e13e5_0.fast5#94610be8-25e4-4a12-980b-2376634ebfe7) Unha ndled exception KeyError: "Can't open attribute (can't locate attribute: 'num_events_template')" Traceback (most recent call last): File "/home/epicardi/bin/miniconda2/envs/py3/lib/python3.6/site-packages/poreplex/signal_analyzer.py", line 114, in process siganal.process() File "/home/epicardi/bin/miniconda2/envs/py3/lib/python3.6/site-packages/poreplex/signal_analyzer.py", line 259, in process events = self.load_events() File "/home/epicardi/bin/miniconda2/envs/py3/lib/python3.6/site-packages/poreplex/signal_analyzer.py", line 315, in load_events events = self.npread.load_fast5_events() File "/home/epicardi/bin/miniconda2/envs/py3/lib/python3.6/site-packages/poreplex/signal_loader.py", line 265, in load_fast5_events bcall = self.fast5.get_basecall() File "/home/epicardi/bin/miniconda2/envs/py3/lib/python3.6/site-packages/poreplex/fast5_file.py", line 142, in get_basecall summary['num_events'] = int(segattrs['num_events_template']) 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/epicardi/bin/miniconda2/envs/py3/lib/python3.6/site-packages/h5py/_hl/attrs.py", line 60, in getitem attr = h5a.open(self._id, self._e(name)) 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/h5a.pyx", line 77, in h5py.h5a.open KeyError: "Can't open attribute (can't locate attribute: 'num_events_template')"
How can I fix this issue?
Many thanks, Ernesto