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hyeshik / poreplex

A versatile sequenced read processor for nanopore direct RNA sequencing
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Illegal instruction --barcoding #28

Open matthew-valentine opened 3 years ago

matthew-valentine commented 3 years ago

I have version 0.5 of poreplex installed both on a work server (linux) and on my own Mac. I am unable to get either of them working.

If I run poreplex on the sever (python 3.7.2), when I try to use the --barcoding option I get the following error:

Illegal instruction (core dumped)

In this case the log file is basically empty (apart from the 'Analysis settings' section). If I run it without the --barcoding option it seemingly starts to run, but the progress bar remains stuck on 0% for however long I run it.

On my Mac (python 3.8) if I run it with the --barcoding option, I get the following error:

ERROR: [signal_analyzer.py:48] Unhandled exception NotImplementedError: Cannot convert a symbolic Tensor (bidirectional_2/forward_lstm_1/strided_slice:0) to a numpy array. This error may indicate that you're trying to pass a Tensor to a NumPy call, which is not supportedException in thread QueueManagerThread

I have uploaded the log file for this run in case it is informative.

poreplex.log

Ideally I want to be running this on the linux server as that is where we do most of my work, so if you have any ideas of how to get it working with --barcoding that would be great!

matthew-valentine commented 3 years ago

Update:

I have managed to get poreplex "running" on the linux server now. I now get the same error that I get when running locally, about being unable to convert a symbolic Tensor to a numpy array.