poreplex 0.5, FileNotFoundError: template_median69pA.model does not exist

[taras2706]

Hi, I've installed poreplex 0.5 using: git clone https://github.com/hyeshik/poreplex.git cd poreplex python3 setup.py install

I am using Ubuntu 20.04 terminal on Windows, python3.8.2

Trying to run the command: poreplex --polya -i path/to/fast5_albacore_basecalled/ -o path/to/output I got: ERROR: [signal_analyzer.py:48] Unhandled exception FileNotFoundError: [Errno 2] File /usr/local/lib/python3.8/dist-packages/poreplex-0.5-py3.8-linux-x86_64.egg/poreplex/kmer_models/r9.4_180mv_70bps_5mer_RNA/template_median69pA.model does not exist: '/usr/local/lib/python3.8/dist-packages/poreplex-0.5-py3.8-linux-x86_64.egg/poreplex/kmer_models/r9.4_180mv_70bps_5mer_RNA/template_median69pA.model'Exception in thread QueueManagerThread: 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 "/usr/lib/python3.8/concurrent/futures/process.py", line 394, in _queue_management_worker work_item.future.set_exception(bpe) File "/usr/lib/python3.8/concurrent/futures/_base.py", line 539, in set_exception raise InvalidStateError('{}: {!r}'.format(self._state, self)) concurrent.futures._base.InvalidStateError: CANCELLED: <Future at 0x7f51ffca8d00 state=cancelled> Traceback (most recent call last): File "/usr/local/bin/poreplex", line 11, in <module> load_entry_point('poreplex==0.5', 'console_scripts', 'poreplex')() File "/usr/local/lib/python3.8/dist-packages/poreplex-0.5-py3.8-linux-x86_64.egg/poreplex/commandline.py", line 410, in __main__ main(args) File "/usr/local/lib/python3.8/dist-packages/poreplex-0.5-py3.8-linux-x86_64.egg/poreplex/commandline.py", line 314, in main procresult = ProcessingSession.run(config, logger) File "/usr/local/lib/python3.8/dist-packages/poreplex-0.5-py3.8-linux-x86_64.egg/poreplex/pipeline.py", line 563, in run sess.loop.run_until_complete(task) File "/usr/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete return future.result() asyncio.exceptions.CancelledError

I tried to install the package conventionally by pip3 install poreplex and via source code from the last release, but the same error produced.

I also tried to locate kmer_models downloaded from the repository in the /usr/local/lib/python3.8/dist-packages/poreplex-0.5-py3.8-linux-x86_64.egg/poreplex/ I renamed the folder directly to kmer_models, but still the same error produced.

I was also going to try it with python 3.6 (pip3.6 install poreplex-0.5-cp36-cp36m-manylinux1_x86_64.whl), however, pomegranate package needed for poreplex cannot be installed with the python 3.6.

What might be wrong? Could you help, please?

Also, it is noted that poreplex can internally call the basecaller core routines of albacore, but as soon as I know albacore doesn't support the current version of kit-flowcell combination for DRS (e.g. FLO-MIN106 flowcell + SQK-RNA002 kit cannot be analyzed by albacore according to official documentation). Could it impact the quality of analysis when we use --basecall with data obtained from not compatible kit+flowcell combination? And I have found only the albacore package for the python3.6 or older. Assuming poreplex can only be installed on python3.8 (because of pomegranate), will the --basecall work?

Thank you in advance!