Snakemake (MissingOutputException) doesn't seem to find output files.
1
0
Entering edit mode
5 weeks ago
jkkim ▴ 30

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
        """
Snakemake • 109 views
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2
Entering edit mode
5 weeks ago

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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0
Entering edit mode

Oh...silly me. Than you so much!

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