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getrandom error with pod5 convert fast5 #116
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hi @cocvincent, and then share the Kind regards, |
Hello, And here 4 .log files generated: 2024-03-01--14-02-51-main-pod5.log Sorry, the last file is too big for a simple screenshot. |
Hi @cocvincent - can you try and run # Create a new virtual environment called "venv"
python3.12 -m venv venv --prompt=pod5
# Activate the venv
source venv/bin/activate
# update pip and install pod5
pip install -U pip pod5==0.3.6
# run your command
POD5_DEBUG=1 pod5 convert fast5 ... Kind regards, |
@cocvincent, do you have any updates on this issue? |
Hello @HalfPhoton , Thanks ! |
Hello, Thanks |
Potentially. I suggest giving it a try. Can your cluster administrators update python? If your cluster doesn't have support for python3.8+ then many things will slowly stop working as 3.7 had it's end of life last October. Kind regards, |
Hello, The cluster administrator installed python 3.12 and then pod5 with PIP. It's very similar to what I've had before. Thank you for your time. |
Thanks for the update - we'll take a look at this and get back to you. |
@cocvincent - Can you share some information on your system OS etc? |
Hello, here's the information on OS: NAME="SLES" Unfortunately, it's not possible to update the OS version. Is there a docker image available? Thanks. |
Could you tell me your glibc version? |
The glibc version is 2.19 |
Ok - this reminded me of this similar issue The glibc version you have is too old: #63 (comment) Are you able to compile the project yourself? https://pod5-file-format.readthedocs.io/en/latest/docs/install.html#installation-from-source |
Hello,
I have a problem when trying to convert fast5 files to pod5 files with pod5 convert fast5 (pod5 v0.3.6).
![fonction_erreur_01-03-24](https://private-user-images.githubusercontent.com/161732564/309261159-d6d1f551-c8e7-42ba-b587-b61ac7cc6166.PNG?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjU2NTQ1OTYsIm5iZiI6MTcyNTY1NDI5NiwicGF0aCI6Ii8xNjE3MzI1NjQvMzA5MjYxMTU5LWQ2ZDFmNTUxLWM4ZTctNDJiYS1iNTg3LWI2MWFjN2NjNjE2Ni5QTkc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwOTA2JTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDkwNlQyMDI0NTZaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT0zMjFhYzI3OWY0ZDJlMDhiMjVjZWZkZDIwYjcxYmMzNjUyMjM3ZGU0YzUxZDdlODk1Y2NkNDU4ODNjOTkxZGE3JlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.lhxYzdIhxM6cMgbrtgofO1z53GYWNbpRqn58Ky9vlTE)
In both cases, I get this error in the log file:
![erreur_01-03-24](https://private-user-images.githubusercontent.com/161732564/309259415-b46b61ef-f256-40cc-bc94-f5873ecf9a09.PNG?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjU2NTQ1OTYsIm5iZiI6MTcyNTY1NDI5NiwicGF0aCI6Ii8xNjE3MzI1NjQvMzA5MjU5NDE1LWI0NmI2MWVmLWYyNTYtNDBjYy1iYzk0LWY1ODczZWNmOWEwOS5QTkc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwOTA2JTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDkwNlQyMDI0NTZaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT00YWY1YzM5MzgyM2FkYTcyYTA4MzQ3MWMyY2ZlYTI0OTI4NzlkMDE5Zjk2OTNmZDM4NjIyODcxYzdmNzZiY2NhJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.HqwuZFBBAVgzOqpSjMNHHajpnN65wUWuGJMHP580v2E)
The job is not killed when the error occurs.
I'm using 100G of memory with 50 cpu on a computing cluster.
I hope you can help me, thanks.
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