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

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

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

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

rule fastqc:
      f1 = config['datadirs']['fastq'] + "/" + "{file}_{read}.fq.gz"
   output: config['datadirs']['qc'] + "/" + "{file}_{read}.fastqc.html", config['datadirs']['qc'] + "/" + "{file}_{read}"
   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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 854 users visited in the last hour