Snakemake MissingExceptionOutput
Please, does not anyone know why this code is giving "MissingOutputException" in Snakemake even though the dry-run worked fine.
rule all:
input:
expand(os.path.join(config["input_dir"], "input/{sample}.txt"), sample = ["A","B"]),
rule create_file:
output:
os.path.join(config["input_dir"], "input/{sample}.txt"),
log:
os.path.join(config["log_dir"], "input/{sample}.log"),
shell:
'echo {wildcards.sample} > {output}'
Error:
MissingOutputException in line 8 of /yates_CNV_after_merging/rules/cnv.smk
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
verifyBAMID in snakemake script error
written by Peter Chung
-
Error in snakemake with working shell script
written by Cathy •
-
Snakemake not executing any tasks
written by jaime alvarez •
-
Snakemake error
written by kamanovae •
-
Snakemake does not give output files. Gives no errors
written by kamanovae •
-
snakemake truncating shell codes
written by ohu20a •
-
Snakemake Megahit error
written by blackadder •
-
Snakemake Checkpoints Aggregate issues
written by susheelbhanu •
-
.genome file not found for SnpEff
written by moldach686 •
-
snakemake and Star aligner code issue
written by lawrence.hsu •
I cannot reproduce your issue. I copied your two rules to file
Snakefileand executed it withsnakemake -j 1 -C log_dir='.' input_dir='.'and it completed without errors. Maybe there is something you are not showing?Error refers
cnv.smk. Please post the contents of cnv.smk.