problem in running v0.13.1

[ospfsg]

Hi

after installing the v0.13.1

[ospfsg]

Hi

After installing v0.13.1. I run the command I used to run in version 12 with the new config file adapted. I attached the log file. 2024-10-06T112814.831312.log

I get two error messages. The first related with snakemake. I checked your issues #2957 and it should not be a reason for the pipeline not running or is it ?

second error is new and is related creation of conda envs....

do you mind to check the log file ? thank you osp

[lczech]

Hi @ospfsg,

The first issue you mention (https://github.com/snakemake/snakemake/issues/2957) can likely be ignored, as that is some Snakemake-internal warning, but does not seem to affect the runs.

The second one is new, and only seems to exist since a week. Quick google search revealed that other people have reported this already in the main Snakemake repository (https://github.com/snakemake/snakemake/issues/3108). That seems yet again to be one of those utterly annoying things where the whole conda/mamba ecosystem breaks backwards compatibility... honestly, if I had known that conda and mamba cause so much trouble, I would not have started using it... but well, it is what it is.

As this is an issue between Snakemake and mamba, I cannot do anything as far as grenepipe is concerned to solve this. You can try to downgrade mamba to an older version, or use micromabma instead to set up your environment for grenepipe.

Let me know how that goes :-) Lucas

[ospfsg]

Hi

After installing v0.13.1. I run the command I used to run in version 12 with the new config file adapted. I attached the log file. 2024-10-06T112814.831312.log

I get two error messages. The first related with snakemake. I checked your issues #2957 and it should not be a reason for the pipeline not running or is it ?

second error is new and is related creation of conda envs....

do you mind to check the log file ? thank you osp

Hi @ospfsg,

The first issue you mention (snakemake/snakemake#2957) can likely be ignored, as that is some Snakemake-internal warning, but does not seem to affect the runs.

The second one is new, and only seems to exist since a week. Quick google search revealed that other people have reported this already in the main Snakemake repository (snakemake/snakemake#3108). That seems yet again to be one of those utterly annoying things where the whole conda/mamba ecosystem breaks backwards compatibility... honestly, if I had known that conda and mamba cause so much trouble, I would not have started using it... but well, it is what it is.

As this is an issue between Snakemake and mamba, I cannot do anything as far as grenepipe is concerned to solve this. You can try to downgrade mamba to an older version, or use micromabma instead to set up your environment for grenepipe.

Let me know how that goes :-) Lucas

Dear Lucas thank for your reply.

I go to install micromamba, but then I should keep the same option in the snakemake command: --use-conda --conda-frontend mamba --conda-prefix .../conda-envs/

or change to:

--use-micromamba --conda-frontend micromamba ...

thank you osp

[lczech]

Hi @ospfsg,

the command should be the same, i.e., --use-conda --conda-frontend mamba. The way to get snakemake to use micromamba is by using micromamba to install the grenepipe environment, activate that environment, and then run grenepipe as usual from there. See here.

Cheers Lucas

[lczech]

Hi Octavio,

is this issue solved then, given the new issue in #58? Let me know if we can close this, or if you have further questions :-)

Cheers Lucas

[lczech]

Okay, I assume we can close this then :-)

If not, as always, feel free to comment, re-open, or start a new issue!

Cheers Lucas