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nanoporetech / ont_fast5_api

Oxford Nanopore Technologies fast5 API software
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Multi to single fast5 goes into sleep #63

Closed kaltinel closed 2 years ago

kaltinel commented 2 years ago

Hi,

I am trying to convert my multi fast5 into singular ones to run Tombo with it. However, my jobs are getting into S and D state and nothing happens. Screenshot from 2021-10-20 12-01-00

My command is:

multi_to_single_fast5 -i $multi_read_fast5_dir -s $single_read_fast5_dir -t 10 --recursive
| 0 of 88|  |  0% ETA:  --:--:--

I installed dependencies with pip, on conda environment. h5py-3.1.0 numpy-1.19.5 ont-fast5-api-4.0.0

I would appreciate some help. Thanks!

fbrennen commented 2 years ago

Hi @kaltinel -- what happens if you set the number of threads to 1? (-t 1)

kaltinel commented 2 years ago

Thanks for your reply.

The same behaviour happens with one thread.

multi_to_single_fast5 -i $multi_read_fast5_dir -s $single_read_fast5_dir -t 1 --recursive
| 0 of 88| |  0% ETA:  --:--:--

same

fbrennen commented 2 years ago

Great, thanks for checking. Where are you storing your input and output files? Are they local to the machine, or stored somewhere on a network?

kaltinel commented 2 years ago

They are stored somewhere in the network (using a server)

fbrennen commented 2 years ago

Fab, ok -- can you try moving one or two files locally and see if it works? That would help eliminate network I/O issues.

kaltinel commented 2 years ago

Hm.. It worked.. I tried with one file in the directory as an example.

multi_to_single_fast5 -i FAST5_EXAMPLE/ -s SINGLE/ --recursive
| 4000 of 4000|##########################################################################################################################################################################|100% Time: 0:00:04

I do not know how to get pass I/O issues in the server though.

fbrennen commented 2 years ago

Great to hear that it's working. =) It sounds like you've got some network issues to resolve then, which are independent of the tools. I'm afraid I don't know how to solve those -- I would suggest checking with whoever administers your network. I'm sorry I can't be of more help -- hopefully it's an easy fix!