Closed:RNA-SEQ Snakemake error

Question

[arshil]

Hi everyone, can someone help me out with the error. i am running the following code for my fastq files, when i run , only the fastqc rule is excuted and its says job completed, my two other rules for trimming and fastqc for trimmed files doesnt get executed. i am pretty new to bioinformatics. my codes looks like.

SAMPLES, = glob_wildcards("/scratch/mk9uc/RNA_Seq/{sample}_1.fastq.gz")
READS=["1", "2"]

rule fastqc_raw:
   input:  "/scratch/mk9uc/RNA_Seq/{sample}_{read}.fastq.gz"
   output: "qc_outputt/{sample}_{read}_fastqc.html"
   shell: """
      module load fastqc
      mkdir -p  qc_outputt
      fastqc --outdir qc_outputt --thread 8 --nogroup {input}
         #    >> /scratch/mk9uc/RNA_Seq/fastqc.log 2>>{log}
        """

rule trimming:
    input:
    fwd = "/scratch/mk9uc/RNA_Seq/{sample}_1.fastq.gz",
        rev = "/scratch/mk9uc/RNA_Seq/{sample}_2.fastq.gz"
    output:
    fwd_paired = "seqs_trimmedd/{sample}_trimmed_1.fastq.gz",
        rev_paired = "seqs_trimmedd/{sample}_trimmed_2.fastq.gz",
    params:
       PAIR = "PE SE".split(),
       TRIM_OPTS = " -threads 16 -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36"

    shell: """
         module load trimmomatic
         mkdir -p seqs_trimmedd
         java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.36.jar \
            {params.PAIR[0]} {input.fwd} {input.rev} \
            {output.fwd_paired}  \
            {output.rev_paired}  \
            {params.TRIM_OPTS}
        """
rule fastqc_trimmed:
   input:  "/scratch/mk9uc/RNA_Seq/seqs_trimmedd/{sample}_trimmed_{read}.fastq.gz"
   output: "trimmedd/qc_output/{sample}_{read}_fastqc.html"
   shell: """
      module load fastqc
      mkdir -p qc_trimmedd
      fastqc --outdir qc_trimmedd --thread 8 --nogroup {input}
         #    >> /scratch/mk9uc/RNA_Seq/fastqc.log 2>>{log}
        """
rule mytarget:
   input: expand("qc_outputt/{sample}_{read}_fastqc.html", sample=SAMPLES, read=READS)
   input: expand("seqs_trimmedd/{sample}_trimmed_{read}.fastq.gz", sample=SAMPLES, read=READS)
   input: expand("qc_trimmedd/{sample}_{read}_fastqc.html", sample=SAMPLES, read=READS)