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nanoporetech / ont_fast5_api

Oxford Nanopore Technologies fast5 API software
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mounting error #52

Closed xj-Liang-Olga closed 3 years ago

xj-Liang-Olga commented 3 years ago

Hello, I have some questions in this part. I have installed the ont-fast5-api:

$pip3 install ont-fast5-api Requirement already satisfied: ont-fast5-api in .../python3.8/site-packages (3.3.0) Requirement already satisfied: packaging in .../python3.8/site-packages (from ont-fast5-api) (20.8) Requirement already satisfied: h5py>=2.8 in .../python3.8/site-packages (from ont-fast5-api) (3.1.0) Requirement already satisfied: progressbar33>=2.3.1 in .../python3.8/site-packages/progressbar33-2.4-py3.8.egg (from ont-fast5-api) (2.4) Requirement already satisfied: numpy>=1.16 in .../python3.8/site-packages (from ont-fast5-api) (1.19.1) Requirement already satisfied: pyparsing>=2.0.2 in .../python3.8/site-packages/pyparsing-3.0.0b2-py3.8.egg (from packaging->ont-fast5-api) (3.0.0b2)

But an error occurred at run time:

$multi_to_single_fast5 -h Traceback (most recent call last): File "/home/li/.local/bin/multi_to_single_fast5", line 5, in from ont_fast5_api.conversion_tools.multi_to_single_fast5 import main File "/home/li/.local/lib/python2.7/site-packages/ont_fast5_api/init.py", line 10, in from ont_fast5_api.compression_settings import register_plugin File "/home/li/.local/lib/python2.7/site-packages/ont_fast5_api/compression_settings.py", line 73 raise IOError(VBZ_ERROR_MESSAGE.format(register_plugin())) from err ^ SyntaxError: invalid syntax

Could you give me some adivice?

fbrennen commented 3 years ago

Hi @Xiaojuan-Liang -- as you can see from your traceback, you have managed to install ont-fast5-api as a Python 2 package:

File "/home/li/.local/lib/python2.7/site-packages/ont_fast5_api/init.py"

You will need to uninstall it from there first -- I think pip uninstall --user ont-fast5-api should work.

xj-Liang-Olga commented 3 years ago

OK, thanks for your reply, let me have a try.