more problems with version 0.13.1

[ospfsg]

Dear Lucas

Finally I try to run grenepipe after installing the environment with micromamba.

I update the config file and add the relevant information as I did with previous version that I run in version 0.12.

But this time
2024-10-21T111227.306719.snakemake.log it stops in early stage....I attached the log file.

I have this messages:

any suggestion?

thank you osp

[lczech]

Hi Octavio,

hm, I think I have seen this one before, but can't quite remember. The log file you appended is the regular one from Snakemake, right? Unfortunately, the Snakemake version we are currently using does not print my custom grenepipe header to the log file, which however contains important information for me to debug this. Could you please also attach the log file for this run that is stored in the working directory of your run, under logs/snakemake?

My best guess with the information that I have right now is that somehow, the base conda environment from which you run grenepipe has a conflicting numpy version. Are you calling grenepipe with the conda environment active that you used for a previous version of grenepipe? That likely will not work. You will have to follow the Preparing the environment steps again, and create a new environment which contains the updated versions of everything. For this, you can either delete the previous grenepipe conda environment, or, what I like to do, is create a new one with a new name.

For instance, the way that I set this up is using the following command to create the env:

micromamba env create -f workflow/envs/grenepipe.yaml -n grenepipe-v0.13.1

The difference to the documented command is the suffix with the grenepipe version for the name (option -n) of the environment. Before running this command, make sure to deactivate any other environments that you might be in (micromamba deactivate). After that, you need to activate that particular environment of course (using the name that you gave it above).

Let me know if that solves the issue.

Cheers Lucas

[ospfsg]

First I attached the log file you ask. 2024-10-21T111226.651528.log

Second: I removed the previous grenepipe env

conda env remove -n grenepipe

then I instaled micromamba

"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

micromamba self-update

Your micromamba version (2.0.2) is already up to date.

then create and activate a conda environment for running snakemake. cd /path/to/grenepipe

micromamba env create -f workflow/envs/grenepipe.yaml

micromamba activate grenepipe

and then I run the command: (grenepipe) dau1@frey:~/software/grenepipe-0.13.1$ snakemake --use-conda --conda-frontend mamba --cores 102 --directory /mnt/data3/Project_KeePace/Operational/4_data_analysis/5_grenepipe/run5/ --conda-prefix /home/dau1/software/conda-envs/

my installation env create is different since I didn´t add the -n grenepipe-v0.13.1.

but: 1 -I removed the previous conda env grenepipe, in miniconda3/envs there is no trace of grenepipe 2- I installed micromamba for the first time. The grenepipe env is there, and is so far the only env there

do you still think that is the -n stuff? I can remove and create again the environment.

osp