syntax error in medaka_consensus

JDKling commented 2 years ago

I am running into an error after calling medaka_consensus.

I am using a pip install (version 1.6.0) and getting the following error from calling medaka_consensus -h

2022-04-29 22:07:50.917262: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2022-04-29 22:07:50.917304: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
  File "<string>", line 1
    import sys; import itertools; mods=[f'{x[:-1]}' for x in sys.stdin.readline().split() if ('variant' not in x and 'snp' not in x)]; print(' '.join(mods))
                                                  ^
SyntaxError: invalid syntax

Compiling from source also gave the same error. Any help on this would be greatly appreciated!

JDKling commented 2 years ago

This turned out to be an issue in with my python path so going to close it.

cjw85 commented 2 years ago

Glad we could help! 😉

For anyone else, I suspect the issue was caused by using an older version of python which does not support the f-string syntax.

nanoporetech / medaka

syntax error in medaka_consensus #369