pod5 convert fast5 error, currently using python 3.10 and singularity 3.10.4

[hilo1]

Attempted to convert one fast5 file to test pod5 functionality on our current system

Used standard convertfast5 command and then used the POD5_DEBUG=1 additional to generate additional a log that I'm sharing here. I'm hoping it is something silly like I have an older version of python also loaded and that might be interfering.

Logs

Singularity> pod5 convert fast5 PAW59116_pass_2cfaf0b1_98202c91_9986.fast5 --output converted9986.pod5
An unexpected error occurred: getrandom
Converting 1 Fast5s: 0%| | 0/4000 [00:03<?, ?Reads/s]
POD5 has encountered an error: 'getrandom'

For detailed information set POD5_DEBUG=1'
Converting 1 Fast5s: 0%| | 0/4000 [00:03<?, ?Reads/s]
Singularity> POD5_DEBUG=1 pod5 convert fast5 PAW59116_pass_2cfaf0b1_98202c91_9986.fast5 --output converted9986.pod5
An unexpected error occurred: getrandom
Converting 1 Fast5s: 0%| | 0/4000 [00:01<?, ?Reads/s]Traceback (most recent call last):
File "/usr/local/bin/pod5", line 8, in
sys.exit(main())
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/main.py", line 60, in main
return run_tool(parser)
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/parsers.py", line 41, in run_tool
raise exc
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/parsers.py", line 38, in run_tool
return tool_func(**kwargs)
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/parsers.py", line 137, in run
return convert_from_fast5(**kwargs)
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/utils.py", line 63, in wrapper
raise exc
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/utils.py", line 60, in wrapper
ret = func(*args, **kwargs)
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/pod5_convert_from_fast5.py", line 826, in convert_from_fast5
raise exc
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/pod5_convert_from_fast5.py", line 810, in convert_from_fast5
process_conversion_tasks(
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/utils.py", line 63, in wrapper
raise exc
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/utils.py", line 60, in wrapper
ret = func(*args, **kwargs)
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/pod5_convert_from_fast5.py", line 741, in process_conversion_tasks
writer = output_handler.get_writer(path)
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/utils.py", line 63, in wrapper
raise exc
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/utils.py", line 60, in wrapper
ret = func(*args, **kwargs)
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/pod5_convert_from_fast5.py", line 241, in get_writer
return self._open_writer(output_path=output_path)
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/utils.py", line 63, in wrapper
raise exc
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/utils.py", line 60, in wrapper
ret = func(*args, **kwargs)
File "/usr/local/lib/python3.10/dist-packages/pod5/tools/pod5_convert_from_fast5.py", line 227, in _open_writer
writer = p5.Writer(output_path)
File "/usr/local/lib/python3.10/dist-packages/pod5/writer.py", line 108, in init
self._writer: Optional[p5b.FileWriter] = p5b.create_file(
RuntimeError: getrandom
Converting 1 Fast5s: 0%| | 0/4000 [00:01<?, ?Reads/s]

Specifications

• Pod5 Version: 0.3.12
• Python Version: 3.10
• Singularity Version: 3.10.4
• Platform: GNU/Linux X86-64

[HalfPhoton]

The error: RuntimeError: getrandom
Is from the GLIBC getrandom function (docs) which is available from in versions Linux 3.17, glibc 2.25.

Can you please check your linux kernel version uname -r?

Best regards,
Rich

[hilo1]

Thanks for your swift response Rich! I think I have to beg my systems administrator for an update

Here's the result:
3.10.0-514.2.2.el7.x86_64

Best,
Noe

[HalfPhoton]

Hi Noe, no problem!

Yeah, it looks like this is the underlying issue.
It might be possible to get a suitable glibc version within your singularity or docker container though. Although I'm not sure on the details on achieving this.

Best regards,
Rich