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nanoporetech / ont_fast5_api

Oxford Nanopore Technologies fast5 API software
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fail to run fast5_subset #17

Closed limin321 closed 5 years ago

limin321 commented 5 years ago

My data are nanopore data, and I convert all fast5 data to multi-read using single_to_multi_fast5. Then I want to extract all fast5 reads that belong to one bacterium strain together by running the following command: fast5_subset --input ./multi_reads/ --save_path ./rub_server_fast5 --read_id_list ./rub/BC11_rub_headers.txt --recursive

However, it failed with the following informaiton: Traceback (most recent call last): File "/afs/genomecenter.ucdavis.edu/home/limchen/.local/bin/fast5_subset", line 10, in sys.exit(main()) File "/home/limchen/.local/lib/python2.7/site-packages/ont_fast5_api/conversion_tools/multi_fast5_subset.py", line 288, in main recursive=args.recursive, file_list_file=args.file_list) File "/home/limchen/.local/lib/python2.7/site-packages/ont_fast5_api/conversion_tools/multi_fast5_subset.py", line 33, in init assert path.isdir(input_folder) AssertionError

Though it does produce some data and store in the output folder--rub_server_fast5, I still get the above information. Can anyone explain to me what is the problem with my fast5_subset, and how to solve it.

Your help are greatly appreciated. Thank you so much in advance.

fbrennen commented 5 years ago

Hi @limin321 -- the error above suggests that your input path ./multi_reads/ is not a directory. Can you check and make sure it exists, and has the correct name?

fbrennen commented 5 years ago

Hi @limin321 -- is your file conversion working now?

limin321 commented 5 years ago

Hi @limin321 -- is your file conversion working now?

Hi fbrennen,

Thank you for asking again.
I double check multi_reads. It is a directory and has the files, here is the picture.

Screen Shot 2019-07-08 at 12 05 17 PM
fbrennen commented 5 years ago

Great, thanks. What does the output folder look like? Did you get the reads you expected there, or are some missing?

limin321 commented 5 years ago

attached is the information running failed again. here is output folder, the size is not right, only 512. [image: Screen Shot 2019-07-09 at 8.57.26 AM.png]

On Tue, Jul 9, 2019 at 4:23 AM Forrest Brennen notifications@github.com wrote:

Great, thanks. What does the output folder look like? Did you get the reads you expected there, or are some missing?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nanoporetech/ont_fast5_api/issues/17?email_source=notifications&email_token=AKGHTXILUSBVNBFQ65FLNM3P6RYMJA5CNFSM4H4JNCVKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZP6ZKI#issuecomment-509602985, or mute the thread https://github.com/notifications/unsubscribe-auth/AKGHTXOIS5WTR3K3YSAGZVLP6RYMJANCNFSM4H4JNCVA .

fbrennen commented 5 years ago

Hi @limin321 -- just continuing to check in to this. Can you send me a screenshot of the full command you used to run fast5_subset, including the folder you ran it in? (The screenshot you sent in your previous email reply didn't actually show up, by the way.) And can you confirm the version of ont-fast5-api you're using?