Open hilo1 opened 1 month ago
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
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
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
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
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]
Converting 1 Fast5s: 0%| | 0/4000 [00:01<?, ?Reads/s]Traceback (most recent call last): File "/usr/local/bin/pod5", line 8, in
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