Segmentation fault (core dumped) when trying to run pod5 convert fast5
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Hello,
I'm running into a 'Segmentation fault (core dumped)' error every time I try to run pod5 convert fast5 but I cannot figure out why.
I have set POD5_DEBUG=1 but this is not providing any additional information, nor can I find a log file. I was interpreting this as a memory error but I have requested a single CPU with 128Gb memory which surely should be sufficient?
D
@DepledgeLab ,
Can you please provide the command you used?
Kind regards,
Rich
Ah, I'm sure I meant to do that in the first post!
pod5 convert fast5 fast5_pass/*.fast5 --output pod5 --one-to-one fast5_pass/
I also tried it without the one-to-one fast5_pass/ option but had the same result
And you're on the latest pod5 --version?
I'm on version 0.2.4 (which I think is the latest based on running pip install --upgrade pod5)
Interesting - 0.2.4 is not the latest - Can you try and upgrade to 0.3.2?
Curious. Which version of Python is needed for 0.3.2? I have been using v3.8.6 but can't seem to upgrade to a higher version of pod5 with this
Pod5 is available on all actively supported python versions 3.8->3.12
Can you share what error you're seeing while trying to upgrade?
Ach. Fool that I am I just realized the wrong python version (3.7) was being loaded into the environment... I've replaced this with 3.10 and now everything runs just fine.
Apologies for being dim