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arq5x / poretools

a toolkit for working with Oxford nanopore data
MIT License
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Error when reading/handling FAST5 timestamps [Invalid literal for int() with base 10] #152

Closed KJB5200 closed 7 years ago

KJB5200 commented 7 years ago

Trying to analyze LMD run with poretools (v0.5.1) in Py2.7 and keep getting same error when running any commands that require time data (e.g. - yield_plot, squiggle, etc). Here is the traceback from running : File "C:\data\Scripts\poretools-script.py", line 9, in <module> load_entry_point('poretools==0.5.1', 'console_scripts', 'poretools')() File "C:\data\lib\site-packages\poretools\poretools_main.py", line 513, in main args.func(parser, args) File "C:\data\lib\site-packages\poretools\poretools_main.py", line 53, in run_subtool submodule.run(parsers, args) File "C:\data\lib\site-packages\poretools\yield_plot.py", line 72, in run start_time = fast5.get_start_time() File "C:\data\lib\site-packages\poretools\Fast5File.py", line 471, in get_start_time return int(exp_start_time) + int(node.attrs['start_time']) ValueError: invalid literal for int() with base 10: '2017-07-06T14:22:14Z'

The error must lie in the FAST5 files themselves b/c I've run this same function on the test_data and it successfully returned a plot (albeit an unusual one).

KJB5200 commented 7 years ago

Installed poretools-master scripts (found by downloading from here: https://github.com/arq5x/poretools) into directory containing previous poretools build - problem solved!