pod5-file-format getrandom error with pod5 convert fast5

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

In both cases, I get this error in the log file: erreur_01-03-24

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.

Mar 01 '24 12:03 cocvincent

hi @cocvincent, Can you add this environment variable before your command to generate log files please? Please also reduce the number of threads to 2 to generate fewer log files POD5_DEBUG=1 pod5 convert fast5 -t 2 --output outDir/ ...

and then share the .log files generated here?

Kind regards, Rich

Mar 01 '24 13:03 HalfPhoton

Hello, Thank you for your quick reply !

Here is the command: fonction_erreur_POD5_debug_01-03-24

And here 4 .log files generated: erreur_POD5_debug_1_01-03-24

erreur_POD5_debug_2_01-03-24

erreur_POD5_debug_3_01-03-24

2024-03-01--14-02-51-main-pod5.log

Sorry, the last file is too big for a simple screenshot.

Mar 01 '24 14:03 cocvincent

Hi @cocvincent - can you try and run pod5 in a normal python virtual environment please? We've seen a few issues recently with users running in conda.

# 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, Rich

Mar 04 '24 11:03 HalfPhoton

@cocvincent, do you have any updates on this issue?

Mar 11 '24 15:03 HalfPhoton

Hello @HalfPhoton , I have forwarded the request for installation on the cluster. I'm waiting for a reply and will keep you informed.

Thanks !

Mar 11 '24 15:03 cocvincent

Hello, The version of Python on our computing cluster is too old to install pod5 directly. Is using a conda environment and installing pod5 via pip a viable option?

Thanks

Mar 14 '24 08:03 cocvincent

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, Rich

Mar 14 '24 14:03 HalfPhoton

Hello,

The cluster administrator installed python 3.12 and then pod5 with PIP. I tried: fonction_erreur_POD5_debug_15-03-24 and got 4 outputs: erreur_POD5_debug_2_15-03-24 erreur_POD5_debug_3_15-03-24 2024-03-15--08-27-54-main-pod5.log

It's very similar to what I've had before.

Thank you for your time.

Mar 15 '24 09:03 cocvincent

Thanks for the update - we'll take a look at this and get back to you.

Mar 19 '24 12:03 HalfPhoton

@cocvincent - Can you share some information on your system OS etc?

Mar 19 '24 15:03 HalfPhoton

Hello,

here's the information on OS: cat /etc/os-release

NAME="SLES" VERSION="12-SP1" VERSION_ID="12.1" PRETTY_NAME="SUSE Linux Enterprise Server 12 SP1" ID="sles" ANSI_COLOR="0;32" CPE_NAME="cpe:/o:suse:sles:12:sp1"

Unfortunately, it's not possible to update the OS version.

Is there a docker image available?

Thanks.

Mar 20 '24 10:03 cocvincent

Could you tell me your glibc version?

Mar 20 '24 11:03 HalfPhoton

The glibc version is 2.19

Mar 20 '24 11:03 cocvincent

Ok - this reminded me of this similar issue https://github.com/nanoporetech/pod5-file-format/issues/63

The glibc version you have is too old: https://github.com/nanoporetech/pod5-file-format/issues/63#issuecomment-1655312893

Are you able to compile the project yourself? https://pod5-file-format.readthedocs.io/en/latest/docs/install.html#installation-from-source

Mar 20 '24 11:03 HalfPhoton

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getrandom error with pod5 convert fast5

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