libmamba Non-conda folder exists at prefix

[joelive]

When I run the virsorter setup command, it always report error.

(virsort2) bo@bioinofo2:~$ virsorter setup -d virsorter_db/
[2024-10-24 02:47 INFO] VirSorter 2.2.4
[2024-10-24 02:47 INFO] /home/bo/miniconda3/envs/virsort2/bin/virsorter setup -d virsorter_db/
[2024-10-24 02:47 INFO] Setting up VirSorter2 database; this might take ~10 mins and only needs to be done once.
[2024-10-24 02:47 INFO] saving /home/bo/virsorter_db as DBDIR to config file /home/bo/miniconda3/envs/virsort2/lib/python3.10/site-packages/virsorter/template-config.yaml
CreateCondaEnvironmentException:
Could not create conda environment from /home/bo/miniconda3/envs/virsort2/lib/python3.10/site-packages/virsorter/rules/../envs/vs2.yaml:
error libmamba Non-conda folder exists at prefix
critical libmamba Aborting.

File "/home/bo/miniconda3/envs/virsort2/lib/python3.10/site-packages/snakemake/deployment/conda.py", line 350, in create
[2024-10-24 02:47 ERROR] CreateCondaEnvironmentException:
Could not create conda environment from /home/bo/miniconda3/envs/virsort2/lib/python3.10/site-packages/virsorter/rules/../envs/vs2.yaml:
error libmamba Non-conda folder exists at prefix
critical libmamba Aborting.

File "/home/bo/miniconda3/envs/virsort2/lib/python3.10/site-packages/snakemake/deployment/conda.py", line 350, in create
[2024-10-24 02:47 INFO] First attempt failed; trying the second time.
CreateCondaEnvironmentException:
Could not create conda environment from /home/bo/miniconda3/envs/virsort2/lib/python3.10/site-packages/virsorter/rules/../envs/vs2.yaml:
error libmamba Non-conda folder exists at prefix
critical libmamba Aborting.

File "/home/bo/miniconda3/envs/virsort2/lib/python3.10/site-packages/snakemake/deployment/conda.py", line 350, in create
[2024-10-24 02:47 CRITICAL] Command 'snakemake --snakefile /home/bo/miniconda3/envs/virsort2/lib/python3.10/site-packages/virsorter/rules/setup-retry.smk --directory /home/bo/virsorter_db --quiet --config Skip_deps_install=False --jobs 64 --rerun-incomplete --latency-wait 600 --nolock --use-conda --conda-prefix /home/bo/virsorter_db/conda_envs --conda-frontend mamba ' returned non-zero exit status 1.

[ChaoLab]

Hi Jiarong,
I have the same issue as @joelive. I guess it is a conda env setting-up problem.
Can you help to solve this issue?

Best,
Chao

[jiarong]

Sorry, I was quite busy last week.
If you do not have to conda/mamba, I recommend installation option 3. Or else, try to remove the database directory (/home/bo/virsorter_db) and rerun virsorter setup. It looks like there was an failed attempt before.

[handibles]

Seeing this also on a fresh env. After failed installs, there's a conda_envs dir created in the chosen db dir, possibly mamba is attempting to install the setup.smk dependencies alongside the database, which is going awry (i.e. non-conda folder). See line:471 of virsorter.py, and possibly line:155 of setup.smk.

In any case: doing all of the below:

• A fresh mamba env
• deleting the target db dir
• using -s(kip-dependencies) during virsorter setup

allowed setup to complete, but does not allow virsorter to run - the error is ~same as the above:

[2024-10-31 16:21 INFO] /mnt/workspace2/jamie/miniforge3/envs/pha/bin/virsorter run -w /mnt/workspace2/jamie/mtu__phamm/6__virsorter/vsort_SPA_ERR10157887 -i /mnt/workspace2/jamie/mtu__phamm/4__spades/ERR10157887/contigs.fasta --min-length 10000 -j 8                                                                                                     
[2024-10-31 16:21 INFO] Using /mnt/workspace2/jamie/miniforge3/envs/pha/lib/python3.10/site-packages/virsorter/template-config.yaml as config template                                                                                    
[2024-10-31 16:21 INFO] conig file written to /mnt/workspace2/jamie/mtu__phamm/6__virsorter/vsort_SPA_ERR10157887/config.yaml                                                                                                             
                                                                                                                     
[2024-10-31 16:21 INFO] Executing: snakemake --snakefile /mnt/workspace2/jamie/miniforge3/envs/pha/lib/python3.10/site-packages/virsorter/Snakefile --directory /mnt/workspace2/jamie/mtu__phamm/6__virsorter/vsort_SPA_ERR10157887 --jobs 8 --configfile /mnt/workspace2/jamie/mtu__phamm/6__virsorter/vsort_SPA_ERR10157887/config.yaml --latency-wait 600 --rerun-incomplete --nolock  --conda-frontend mamba --conda-prefix /mnt/workspace2/jamie/vdb/conda_envs --use-conda    --quiet  all                                                                                                         
CreateCondaEnvironmentException:                                                                                     
Could not create conda environment from /mnt/workspace2/jamie/miniforge3/envs/pha/lib/python3.10/site-packages/virsorter/rules/../envs/vs2.yaml:                                                                                          
error    libmamba Non-conda folder exists at prefix                                                                  
critical libmamba Aborting.                                                                                          
                                                                                                                     
  File "/mnt/workspace2/jamie/miniforge3/envs/pha/lib/python3.10/site-packages/snakemake/deployment/conda.py", line 350, in create                  

[joelive]

I have solved the problem by mamually mamba install all packages

[handibles]

I have solved the problem by mamually mamba install all packages

@joelive glad it works! My comment above doesn't allow you to run virsorter, as it still attempts a conda-env when you use virsorter run, and then it crashes - did you need to do anything else to stop conda getting upset?

[jiarong]

@ALL, I just had chance to test this. It looks like the new mamba version 2 is the issue. You can change to mamba version 1 to resolve this issue.

# get into the vs2 env
conda activate vs2
# downgrade mamba to v1
mamba installl -c conda-forge mamba=1

[anniedussault]

thanks @jiarong thanks for the solution! I was able to install your app and run it!

[sohini5981]

Hello @jiarong

I have installed vs2 using mamba (ver 1.5.9)
base * /storage/home/svg5863/miniforge3
vs2 /storage/home/svg5863/miniforge3/envs/vs2. However, the problem @joelive faced persists for me. When I try to setup the db folder, the job exists with the following errors:

/storage/home/svg5863/miniforge3/envs/vs2/bin/virsorter setup -d db -j 4
[2024-11-22 13:05 INFO] Setting up VirSorter2 database; this might take ~10 mins and only needs to be done once.
[2024-11-22 13:05 INFO] saving /storage/home/svg5863/db as DBDIR to config file /storage/home/svg5863/miniforge3/envs/vs2/lib/python3.10/site-packages/virsorter/template-config.yaml
CreateCondaEnvironmentException:
Could not create conda environment from /storage/home/svg5863/miniforge3/envs/vs2/lib/python3.10/site-packages/virsorter/rules/../envs/vs2.yaml:
/storage/home/svg5863/miniforge3/envs/vs2/lib/python3.10/argparse.py:1930: FutureWarning: remote_definition is deprecated and will be removed in 25.9. Use conda env create --file=URL instead.
action(self, namespace, argument_values, option_string)
Collecting package metadata (repodata.json): ...working...
File "/storage/home/svg5863/miniforge3/envs/vs2/lib/python3.10/site-packages/snakemake/deployment/conda.py", line 350, in create
[2024-11-22 13:06 ERROR] CreateCondaEnvironmentException:
Could not create conda environment from /storage/home/svg5863/miniforge3/envs/vs2/lib/python3.10/site-packages/virsorter/rules/../envs/vs2.yaml:
/storage/home/svg5863/miniforge3/envs/vs2/lib/python3.10/argparse.py:1930: FutureWarning: remote_definition is deprecated and will be removed in 25.9. Use conda env create --file=URL instead.
action(self, namespace, argument_values, option_string)
Collecting package metadata (repodata.json): ...working...
File "/storage/home/svg5863/miniforge3/envs/vs2/lib/python3.10/site-packages/snakemake/deployment/conda.py", line 350, in create
[2024-11-22 13:06 INFO] First attempt failed; trying the second time.
CreateCondaEnvironmentException:
Could not create conda environment from /storage/home/svg5863/miniforge3/envs/vs2/lib/python3.10/site-packages/virsorter/rules/../envs/vs2.yaml:
/storage/home/svg5863/miniforge3/envs/vs2/lib/python3.10/argparse.py:1930: FutureWarning: remote_definition is deprecated and will be removed in 25.9. Use conda env create --file=URL instead.
action(self, namespace, argument_values, option_string)
Collecting package metadata (repodata.json): ...working...
File "/storage/home/svg5863/miniforge3/envs/vs2/lib/python3.10/site-packages/snakemake/deployment/conda.py", line 350, in create
[2024-11-22 13:07 CRITICAL] Command 'snakemake --snakefile /storage/home/svg5863/miniforge3/envs/vs2/lib/python3.10/site-packages/virsorter/rules/setup-retry.smk --directory /storage/home/svg5863/db --quiet --config Skip_deps_install=False --jobs 4 --rerun-incomplete --latency-wait 600 --nolock --use-conda --conda-prefix /storage/home/svg5863/db/conda_envs --conda-frontend mamba ' returned non-zero exit status 1.
Any advice??

[anniedussault]

@sohini5981 Have you tried the solution here ? #222 (comment)

I had a smilar issue to what you're describing and this resolved my issue. I would start with that!

[jiarong]

@sohini5981 Have you tried the solution here ? #222 (comment)

I had a smilar issue to what you're describing and this resolved my issue. I would start with that!

Right, it's the same issue. The trick is to change mamba within the VS2 env. The problem is the mamba within the VS2 env, not the mamba in your base env.

[sohini5981]

Thank you all for addressing the issue. I did change the mamba ver within the vs2 env. It did not help. Hence, I used the aptainer method to install the whole thing. That worked and hopefully now I will be able to run it. Thank you all.

…

On Fri, Nov 22, 2024, 7:39 PM jiarong ***@***.***> wrote: @sohini5981 <https://github.com/sohini5981> Have you tried the solution here ? #222 (comment) <#222 (comment)> I had a smilar issue to what you're describing and this resolved my issue. I would start with that! Right, it's the same issue. The trick is to change mamba within the VS2 env. The problem is the mamba within the VS2 env, not the mamba in your base env. — Reply to this email directly, view it on GitHub <#222 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJXQUR3ATFKP4AYKA2UA2BD2B7FFBAVCNFSM6AAAAABQQCTYRCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOJVGE2TGMZTG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[jiarong]

@ALL, I have fixed this issue in bioconda version. Just upgarde and you should be able to run w/o manually downgrading mamba to v1.

[bioinfogini]

@jiarong thanks for posting the solution about downgrading mamba when facing libmamba Non-conda folder exists at prefix Error! It worked also for issues not related to VirStorter2, but to Metagenome atlas as well!

[SilasK]

Thank you for the fix. any idea hopw this could be permanently solved. libmamba v1 is no longer maintained and eventually we should swicht to v2..

[jiarong]

My understanding is that the issue is caused by the incompatibility between snakemake and mamba2. We can switch back to conda since it's conda's resolver is pretty decent now, or just wait till snakemake resolve the issue with mamba2.