cademirch
commented
2 months ago This should be fixed in the latest merge. Try pulling main and running again.
On Thu, Apr 18, 2024 at 13:26 Dawson White @.***> wrote:
Hello again, Getting this error in the new update. I have read through the docs but I realize there could be some new different resource config setting within the new snakemake v8 settings that I am failing to modify. The E. coli test works but the dry run for my samplesheet is failing. I have uninstalled and reinstalled with the same results.
Snakemake version
8.10.7
Logs
snakemake --workflow-profile ./profiles/slurm --dry-run
Using workflow specific profile ./profiles/slurm for setting default command line arguments. snpArcher: Using Snakemake 8.10.7
/n/holyscratch01/davis_lab/dwhite/panDryas/snpArcher/workflow/snparcher_utils/init.py:12: FutureWarning: Downcasting behavior in replace is deprecated and will be removed in a future version. To retain the old behavior, explicitly call result.infer_objects(copy=False). To opt-in to the future behavior, set pd.set_option('future.no_silent_downcasting', True) samples = pd.readtable(config["samples"], sep=",", dtype=str).replace(' ', '', regex=True)
KeyError in file /n/holyscratch01/davis_lab/dwhite/panDryas/snpArcher/workflow/rules/common.smk, line 25: 'resource_config' File "/n/holyscratch01/davis_lab/dwhite/panDryas/snpArcher/workflow/rules/common.smk", line 25, in
Minimal example
mamba create -c conda-forge -c bioconda -n snparcher "snakemake>=8" "python==3.11.4" mamba activate snparcher git clone https://github.com/harvardinformatics/snpArcher.git cd snpArcher snakemake -d .test/ecoli --cores 1 --use-conda # works just fine
changed config/config.yaml
sample data sheet: added final prefix: s391v1 bigtemp: ./tmp maf: 0.02 missingness: 0.9
pip install snakemake-executor-plugin-slurm
Changed cluster parameters
nano profiles/slurm/config.yaml retries: 3 slurm_partition: "shared" runtime: 500
modify fastp, add lines to shell command:
/n/holyscratch01/davis_lab/dwhite/snpArcher/workflow/rules/fastq.smk "--trim_front1=5 " "--trim_front2=5 " "--cut_mean_quality=20" "--cut_front " "--cut_tail " "--trim_poly_g " "--trim_poly_x " "--length_required=35 "
Thanks for your attention! Dawson
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tsackton
Erythroxylum
Hello again, Getting this error in the new update. I have read through the docs but I realize there could be some new different resource config setting within the new snakemake v8 settings that I am failing to modify. The E. coli test works but the dry run for my samplesheet is failing. I have uninstalled and reinstalled with the same results.
Snakemake version
8.10.7
Logs
snakemake --workflow-profile ./profiles/slurm --dry-run
Using workflow specific profile ./profiles/slurm for setting default command line arguments. snpArcher: Using Snakemake 8.10.7
/n/holyscratch01/davis_lab/dwhite/panDryas/snpArcher/workflow/snparcher_utils/init.py:12: FutureWarning: Downcasting behavior in replace is deprecated and will be removed in a future version. To retain the old behavior, explicitly call result.infer_objects(copy=False). To opt-in to the future behavior, set pd.set_option('future.no_silent_downcasting', True) samples = pd.readtable(config["samples"], sep=",", dtype=str).replace(' ', '', regex=True)
KeyError in file /n/holyscratch01/davis_lab/dwhite/panDryas/snpArcher/workflow/rules/common.smk, line 25: 'resource_config' File "/n/holyscratch01/davis_lab/dwhite/panDryas/snpArcher/workflow/rules/common.smk", line 25, in
Minimal example
mamba create -c conda-forge -c bioconda -n snparcher "snakemake>=8" "python==3.11.4" mamba activate snparcher git clone https://github.com/harvardinformatics/snpArcher.git cd snpArcher snakemake -d .test/ecoli --cores 1 --use-conda # works just fine
changed config/config.yaml
sample data sheet: added final prefix: s391v1 bigtemp: ./tmp maf: 0.02 missingness: 0.9
pip install snakemake-executor-plugin-slurm
Changed cluster parameters
nano profiles/slurm/config.yaml retries: 3 slurm_partition: "shared" runtime: 500
modify fastp, add lines to shell command: /n/holyscratch01/davis_lab/dwhite/snpArcher/workflow/rules/fastq.smk
"--trim_front1=5 " "--trim_front2=5 " "--cut_mean_quality=20" "--cut_front " "--cut_tail " "--trim_poly_g " "--trim_poly_x " "--length_required=35 "
conda activate snparcher snakemake --workflow-profile ./profiles/slurm --snakefile ./workflow/Snakefile --notemp --dryrun snakemake --workflow-profile ./profiles/slurm --dry-run # also fails
Thanks for your attention! Dawson