Question: missingoutputexception, snakemake after completing 95% analysis
0
gravatar for arshil
9 days ago by
arshil0
arshil0 wrote:

Hi, can anyone look at the code and tell whats wrong with the code. it runs and does fastqc analysis till 95 % and than show missingf output files and stops. can anyone help me out with this .

from util.varsub import varsub
shell.prefix("set -euo pipefail;")
configfile: "config.yaml"
varsub(config)

shell.prefix("source ~/.bash_profile")
freeze = config['freeze']

SAMPLES, = glob_wildcards(config['datadirs']['fastq'] + "/" + "{file}_1.fq.gz")
READS = ["1", "2"]

rule all:
   input:
       expand(config['datadirs']['qc'] + "/" + "{file}_{read}.fastqc.html", file = SAMPLES, read = READS)


rule fastqc:
   input:
      f1 = config['datadirs']['fastq'] + "/" + "{file}_{read}.fq.gz"
   output: config['datadirs']['qc'] + "/" + "{file}_{read}.fastqc.html", config['datadirs']['qc'] + "/" + "{file}_{read}.fastqc.zip"
   shell: """
      mkdir -p qc_output
      fastqc  --thread 8 --outdir qc_output --nogroup {input.f1}
          """
fastqc rna-seq snakemake • 130 views
ADD COMMENTlink modified 9 days ago by Alex Reynolds28k • written 9 days ago by arshil0

Please show us the complete error message you receive.

ADD REPLYlink written 8 days ago by finswimmer11k

It's likely that there's a typo in the the output file name. Just double check that.

ADD REPLYlink written 8 days ago by Devon Ryan91k

thanks, yeah there was issue with the output naming.

ADD REPLYlink written 5 days ago by arshil0

Happens to all of us :)

ADD REPLYlink written 5 days ago by Devon Ryan91k
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