"SyntaxError" reported by medaka_consensus and installing.

[jyw-atgithub]

To whom it may concern, There are two issues.

1. I could not install the Medaka 1.7.2 from Bioconda, even everything was up-to-date and a new environment was created.
2. After days of trails, I used pip to installed the latest version of Medaka on a server with Ubuntu. In the test run, the following command was given.

medaka_consensus -i ....../raw/PRJNA929424/SRR23269563_ONT.fastq -d ....../assemble/SRR23269563_ONT_Flye/assembly.fasta -o ....../SRR23269563-medaka-1/ -t 8 -m r941_min_hac_g507

Then the messages were shown: 2023-03-08 17:28:23.289950: 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 2023-03-08 17:28:23.289989: 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

May I know how to resolve the problems? Thank you!

Environment (if you do not have a GPU, write No GPU):

• Installation method: pypi (pip install)
• OS: Ubuntu 22.04.2 LTS
• medaka version: medaka 1.7.3
• GPU model: NVIDIA GV100 [TITAN V]
• NVIDIA-SMI 470.161.03 Driver Version: 470.161.03 CUDA Version: 11.4
• Python 2.7.18
• Python 3.10.6
• pip 22.0.2 from /usr/lib/python3/dist-packages/pip (python 3.10)`

[cjw85]

The above errors looks to be coming from a Python 2 interpreter. Please ensure that Python 3 is correctly being used when running medaka. To do this we recommend using a virtual environment.

[cjw85]

Closing through lack of response.