Snakemake (MissingOutputException) doesn't seem to find output files.
Hi all,
I am trying snakemake as below, and I obtained what I wanted (Fastqc.html.zip files) but snakemake doesn't seem to find the output files. The below is the a part of the logs.
"MissingOutputException
Job Missing files after 5 seconds:
01.Fastqc/0Hour_001_1.fastqc.html
01.Fastqc/0Hour_001_1.fastqc.zip"
I have tried differently, but I have no idea why it doesn't locate the output files. They are in 01.Fastqc directory.
Thank you all
SAMPLES, = glob_wildcards("data/{sample}_1.fq.gz")
READS = [1,2]
rule all:
input:
expand("01.Fastqc/{sample}_{reads}.fastqc.html", sample=SAMPLES, reads=READS),
expand("01.Fastqc/{sample}_{reads}.fastqc.zip", sample=SAMPLES, reads=READS)
rule fastqc_file:
input:
r1 = 'data/{sample}_1.fq.gz',
r2 = 'data/{sample}_2.fq.gz'
output:
out1 = "01.Fastqc/{sample}_{reads}.fastqc.html",
out2 = "01.Fastqc/{sample}_{reads}.fastqc.zip",
shell:
"""
fastqc {input.r1} {input.r2} --outdir 01.Fastqc
"""
1 answer
script has an issue with fastqc output naming conventions. Try this:
SAMPLES, = glob_wildcards("data/{sample}_1.fq.gz")
READS = [1,2]
rule all:
input:
expand("01.Fastqc/{sample}_{reads}_fastqc.html", sample=SAMPLES, reads=READS),
expand("01.Fastqc/{sample}_{reads}_fastqc.zip", sample=SAMPLES, reads=READS)
rule fastqc_file:
input:
r1 = 'data/{sample}_1.fq.gz',
r2 = 'data/{sample}_2.fq.gz'
output:
out1 = "01.Fastqc/{sample}_{reads}_fastqc.html",
out2 = "01.Fastqc/{sample}_{reads}_fastqc.zip",
shell:
"""
fastqc {input.r1} {input.r2} --outdir 01.Fastqc
"""
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