akcorut
MissingInputException in rule all
Hi, I'm trying to run the flow via snakemake (snakemake --cores all --use-conda ) but I get this error.
https://raw.githubusercontent.com/akcorut/kGWASflow/v1.3.0/workflow/rules/common.smk:98: SyntaxWarning: invalid escape sequence '\ ' https://raw.githubusercontent.com/akcorut/kGWASflow/v1.3.0/workflow/rules/common.smk:99: SyntaxWarning: invalid escape sequence '\ ' https://raw.githubusercontent.com/akcorut/kGWASflow/v1.3.0/workflow/rules/common.smk:100: SyntaxWarning: invalid escape sequence '\ ' https://raw.githubusercontent.com/akcorut/kGWASflow/v1.3.0/workflow/rules/common.smk:101: SyntaxWarning: invalid escape sequence '\ ' https://raw.githubusercontent.com/akcorut/kGWASflow/v1.3.0/workflow/rules/common.smk:102: SyntaxWarning: invalid escape sequence '_'
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| | / ____\ \ / /\ / ____|/ _| |
| | _| | __ \ \ /\ / / \ | (___ | |_| | _____ __
| |/ / | |_ | \ \/ \/ / /\ \ \___ \| _| |/ _ \ \ /\ / /
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kGWASflow: A Snakemake Workflow for k-mers Based GWAS
Date: 2024-04-30 13:55:39
Author: Adnan Kivanc Corut
kGWASflow version: v1.3
Snakemake version: 8.11.1
Python version: 3.12.3
Snakefile: https://raw.githubusercontent.com/akcorut/kGWASflow/v1.3.0/workflow/rules/common.smk
Base directory: /mnt/lustre/scratch/nlsas/home/csic/bbe/ari/Evosex/WGS/Chreni/sexfindr/step_2/kmersgwas/workflow
Working directory: /mnt/lustre/scratch/nlsas/home/csic/bbe/ari/Evosex/WGS/Chreni/sexfindr/step_2/kmersgwas
Config files: /mnt/lustre/scratch/nlsas/home/csic/bbe/ari/Evosex/WGS/Chreni/sexfindr/step_2/kmersgwas/config/config.yaml
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If you use kGWASflow, please cite:
* Corut, A. K. & Wallace, J. G. kGWASflow: a modular, flexible,
and reproducible Snakemake workflow for k-mers-based GWAS.
bioRxiv (2023). https://doi.org/10.1101/2023.07.10.548365
* Voichek, Y., Weigel, D. Identifying genetic variants underlying
phenotypic variation in plants without complete genomes.
Nat Genet 52, 534–540 (2020). https://doi.org/10.1038/s41588-020-0612-7
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Assuming unrestricted shared filesystem usage. Building DAG of jobs... MissingInputException in rule all in file https://raw.githubusercontent.com/akcorut/kGWASflow/v1.3.0/workflow/Snakefile, line 72: Missing input files for rule all: affected files: results/kmers_table/plink/pheno_/mnt/lustre/scratch/nlsas/home/csic/bbe/ari/Evosex/WGS/Chreni/sexfindr/step_2/kmersgwas/config/phenos.tsv/convert_kmers_table_to_plink.done
Any idea of what's happening?
Thank you.
It's been many months, but I want to say I also have this error and I'm trying to figure out what is going wrong.
I'm not sure if I had the same exact issue, but my problem was when I turned on "kmers_table_to_bed" it gave an error for missing the "convert_kmers_table_to_plink.done" file. I've realized that further on in the config file there is a line:
# phenotype file will be used
phenos: [""]
This needs to be filled in with my phenotype name. When I do that, I no longer get the error. Hope this helps if someone else runs into this issue (and should maybe be flagged more explicitly in the config file)