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nanoporetech / ont_fast5_api

Oxford Nanopore Technologies fast5 API software
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multi_to_single_fast5 command give syntax error #41

Closed aman21392 closed 4 years ago

aman21392 commented 4 years ago

command- multi_to_single_fast5 -i /home/aclab/nanopore/control_nanopore/fast5_pass/ -s /home/aclab/nanopore/control_nanopore --recursive

Traceback (most recent call last): File "/home/aclab/.local/bin/multi_to_single_fast5", line 7, in from ont_fast5_api.conversion_tools.multi_to_single_fast5 import main File "/home/aclab/.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/aclab/.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

I don't understand why it give error. I have total 300 .fast5 which were guppy based call. FAL21946_pass_bbdacd72_0.fast5 FAL21946_pass_bbdacd72_1.fast5 FAL21946_pass_bbdacd72_2.fast5 . . . FAL21946_pass_bbdacd72_300.fast5

so i want it to convert into single.fast5 . Please give me suggestion and in advance thank you.

fbrennen commented 4 years ago

Hi @aman21392 -- what version of ont-fast5-api are you using? We don't support python 2 anymore (as it reached its official end of life last year), and that may have something to do with why you're having issues.

aman21392 commented 4 years ago

pip install ont-fast5-api , I download directly from pip so it may be the latest version. I see some comment in your page and i tried command - python3 multi_to_single_fast5 -i /home/aclab/nanopore/control_nanopore/fast5_pass/ -s /home/aclab/nanopore/control_nanopore --recursive But i got an error- python3: can't open file 'multi_to_single_fast5': [Errno 2] No such file or directory So please give some suggestion how to i find solution. Thank you again

fbrennen commented 4 years ago

Great -- it looks like you'll need to re-install ont-fast5-api for python3 specifically. Try this:

python3 -m pip install ont-fast5-api

And then re-run that python3 multi_to_single [...] command.

We'll add a few protections to make it harder to accidentally install ont-fast5-api on python 2.

aman21392 commented 4 years ago

Thanks its working.

fbrennen commented 4 years ago

Great to hear. =)