MissingInputException in rule all

[Jose-LSP]

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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  _     _______          __      _____  __ _                 
 | |   / ____\ \        / /\    / ____|/ _| |                
 | | _| |  __ \ \  /\  / /  \  | (___ | |_| | _____      __  
 | |/ / | |_ | \ \/  \/ / /\ \  \___ \|  _| |/ _ \ \ /\ / /  
 |   <| |__| |  \  /\  / ____ \ ____) | | | | (_) \ V  V /   
 |_|\_\_____|   \/  \/_/    \_\_____/|_| |_|\___/ \_/\_/    

 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

==================================================================================

 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          

==================================================================================

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.

[owensgl]

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.

[owensgl]

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)

[Dkyuan]

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).

I also met this error.
It works for me to go through without this error when I turned off "kmers_table_to_bed"; Thanks for your suggestion.
Could you please give an example about how to fill the line in

# phenotype file will be used
phenos: [""]

since I want to run again with "kmers_table_to_bed" turned on.

Thanks for your help.