Open Jose-LSP opened 4 months ago
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)
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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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/kmerstable/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.