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harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
MIT License
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environment can't be solved #120

Closed Erythroxylum closed 10 months ago

Erythroxylum commented 10 months ago

Hello, I am trying to run snpArcher on the FAS RC shared and intermediate partitions. I had successfully run the pipeline in the past, including the successful completion of building DAG jobs and creating conda environments, but now this error is being thrown. I cloned the repo yesterday. Python v.3.10.9

Here is the err output:

Building DAG of jobs... Creating conda environment workflow/envs/sambamba.yml... Downloading and installing remote packages. Environment for /n/holyscratch01/davislab/dwhite/snpArcher/workflow/rules/../envs/sambamba.yml created (location: .snakemake/conda/d4ce070fd79db94c65585010a0cbce48) Creating conda environment workflow/envs/fastq2bam.yml... Downloading and installing remote packages. Environment for /n/holyscratch01/davislab/dwhite/snpArcher/workflow/rules/../envs/fastq2bam.yml created (location: .snakemake/conda/bd19444950f6d7198b2ef10e58fef0ed) Creating conda environment workflow/modules/qc/envs/admixture.yml... Downloading and installing remote packages. Environment for /n/holyscratch01/davislab/dwhite/snpArcher/workflow/modules/qc/envs/admixture.yml created (location: .snakemake/conda/ad396f6e3cc1ce39333877d85180f4bf) Creating conda environment workflow/envs/bam2vcf.yml... Downloading and installing remote packages. Environment for /n/holyscratch01/davislab/dwhite/snpArcher/workflow/rules/../envs/bam2vcf.yml created (location: .snakemake/conda/abb557a3ad4a64770d7de92755c7727c) Creating conda environment workflow/modules/qc/envs/qc.yml... Downloading and installing remote packages. Environment for /n/holyscratch01/davislab/dwhite/snpArcher/workflow/modules/qc/envs/qc.yml created (location: .snakemake/conda/c7684bc535c943ed3559cb1e722b5d3d) Creating conda environment workflow/modules/qc/envs/subsample_snps.yml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create conda environment from /n/holyscratch01/davis_lab/dwhite/snpArcher/workflow/modules/qc/envs/subsample_snps.yml: Command: mamba env create --quiet --file "/n/holyscratch01/davislab/dwhite/snpArcher/.snakemake/conda/d31b712157bc989ecf6e7c76da46d03f.yaml" --prefix "/n/holyscratch01/davislab/dwhite/snpArcher/.snakemake/conda/d31b712157bc989ecf6e7c76da46d03f" Output: error libmamba Could not open lockfile '/n/sw/Mambaforge-22.11.1-4/pkgs/cache/cache.lock' error libmamba Could not open lockfile '/n/sw/Mambaforge-22.11.1-4/pkgs/cache/cache.lock' Could not solve for environment specs Encountered problems while solving:

The environment can't be solved, aborting the operation

Thanks for the help, Dawson

tsackton commented 10 months ago

I am not able to replicate this error. Can you test to see if you can install the environment outside of the Snakemake pipeline? Or, alternatively, in case it is a filesystem issue, you could try adding --conda-prefix /path/to/subdir/on/home/filesystem to the snakemake command that runs snpArcher. This will install the conda environments in the path you specify after the conda-prefix option instead of on holyscratch.

erikenbody commented 10 months ago

You might also try a mamba clean --all while you're at it

It is odd its trying to create an env with both bcftools and libcblas, when the yaml "subsamplesnps.yaml" only includes bcftools. I can't build an env with those two either, but the environment from snparcher does work Erik

On Thu, Aug 17, 2023 at 6:49 AM Tim Sackton @.***> wrote:

I am not able to replicate this error. Can you test to see if you can install the environment outside of the Snakemake pipeline? Or, alternatively, in case it is a filesystem issue, you could try adding --conda-prefix /path/to/subdir/on/home/filesystem to the snakemake command that runs snpArcher. This will install the conda environments in the path you specify after the conda-prefix option instead of on holyscratch.

— Reply to this email directly, view it on GitHub https://github.com/harvardinformatics/snpArcher/issues/120#issuecomment-1682322895, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADBA3NZLD4J4TNXGD5LFUD3XVYOPFANCNFSM6AAAAAA3UAYHJQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Erythroxylum commented 10 months ago

OK, thanks for those suggestions. I will let you know how it goes.

-Dawson

On Thu, Aug 17, 2023 at 10:23 AM Erik Enbody @.***> wrote:

You might also try a mamba clean --all while you're at it

It is odd its trying to create an env with both bcftools and libcblas, when the yaml "subsamplesnps.yaml" only includes bcftools. I can't build an env with those two either, but the environment from snparcher does work Erik

On Thu, Aug 17, 2023 at 6:49 AM Tim Sackton @.***> wrote:

I am not able to replicate this error. Can you test to see if you can install the environment outside of the Snakemake pipeline? Or, alternatively, in case it is a filesystem issue, you could try adding --conda-prefix /path/to/subdir/on/home/filesystem to the snakemake command that runs snpArcher. This will install the conda environments in the path you specify after the conda-prefix option instead of on holyscratch.

— Reply to this email directly, view it on GitHub < https://github.com/harvardinformatics/snpArcher/issues/120#issuecomment-1682322895>,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/ADBA3NZLD4J4TNXGD5LFUD3XVYOPFANCNFSM6AAAAAA3UAYHJQ>

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/harvardinformatics/snpArcher/issues/120#issuecomment-1682380331, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABLR5LTCX5LPUYHPXXPMO6TXVYSNPANCNFSM6AAAAAA3UAYHJQ . You are receiving this because you authored the thread.Message ID: @.***>

cademirch commented 10 months ago

@Erythroxylum Were you able to resolve this?

Erythroxylum commented 10 months ago

Hello, Yes, it was resolved using mamba clean --all and rebuilding the snpArcher environment.

On Wed, Aug 23, 2023 at 12:41 PM Cade Mirchandani @.***> wrote:

@Erythroxylum https://github.com/Erythroxylum Were you able to resolve this?

— Reply to this email directly, view it on GitHub https://github.com/harvardinformatics/snpArcher/issues/120#issuecomment-1690455783, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABLR5LUPGCH52XTWRPPYRGDXWZFE7ANCNFSM6AAAAAA3UAYHJQ . You are receiving this because you were mentioned.Message ID: @.***>