Hi guys, can anyone help me with the error i am getting when i am running fastqc through snakemake my code runs for a while and suddenly it gives an error. my code looks like this.
SAMPLES, = glob_wildcards("/scratch/mk9uc/RNA_Seq/{sample}_1.fastq.gz")
READS=["1", "2"]
rule fastqc_raw:
input: expand("/scratch/mk9uc/RNA_Seq/{sample}_{read}.fastq.gz", sample=SAMPLES, read=READS)
output: expand("qc_output/{sample}_{read}_fastqc.html", sample=SAMPLES, read=READS)
log: expand("logs/fastqc/{sample}_{read}_raw.fastqc.err", sample=SAMPLES, read=READS)
shell: """
module load fastqc
mkdir -p log/fastqc
mkdir -p qc_output
fastqc --outdir qc_output --thread 8 --nogroup {input} \
>> /scratch/mk9uc/RNA_Seq/fastqc.log 2>>{log}
"""
error which i am getting looks like this.
Error in rule fastqc_raw: jobid: 0 output: qc_output/SRR7058334_1_fastqc.html, qc_output/SRR7058334_2_fastqc.html, qc_output/SRR7058336_1_fastqc.html, qc_output/SRR7058336_2_fastqc.html, , qc_output/SRR7058333_1_fastqc.html, qc_output/SRR7058333_2_fastqc.html log: logs/fastqc/SRR7058334_1_raw.fastqc.err, logs/fastqc/SRR7058334_2_raw.fastqc.err, logs/fastqc/SRR7058339_1_raw.fastqc.err, logs/fastqc/SRR7058339_2_raw.fastqc.err, logs/fastqc/SRR7058333_1_raw.fastqc.err, logs/fastqc/SRR7058333_2_raw.fastqc.err
RuleException: CalledProcessError in line 11 of /sfs/lustre/scratch/mk9uc/RNA_Seq/Snakefile: Command ' set -euo pipefail; module load fastqc mkdir -p log/fastqc mkdir -p qc_output fastqc --outdir qc_output --thread 8 --nogroup /scratch/mk9uc/RNA_Seq/SRR7058334_1.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058334_2.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058336_1.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058336_2.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058335_1.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058335_2.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058338_1.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058338_2.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058332_1.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058332_2.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058331_1.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058331_2.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7064063_1.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7064063_2.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058339_1.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058339_2.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058333_1.fastq.gz /scratch/mk9uc/RNA_Seq/SRR7058333_2.fastq.gz >> /scratch/mk9uc/RNA_Seq/fastqc.log 2>>logs/fastqc/SRR7058334_1_raw.fastqc.err logs/fastqc/SRR7058334_2_raw.fastqc.err logs/fastqc/SRR7058336_1_raw.fastqc.err logs/fastqc/SRR7058336_2_raw.fastqc.err logs/fastqc/SRR7058335_1_raw.fastqc.err logs/fastqc/SRR7058335_2_raw.fastqc.err logs/fastqc/SRR7058338_1_raw.fastqc.err logs/fastqc/SRR7058338_2_raw.fastqc.err logs/fastqc/SRR7058332_1_raw.fastqc.err logs/fastqc/SRR7058332_2_raw.fastqc.err logs/fastqc/SRR7058331_1_raw.fastqc.err logs/fastqc/SRR7058331_2_raw.fastqc.err logs/fastqc/SRR7064063_1_raw.fastqc.err logs/fastqc/SRR7064063_2_raw.fastqc.err logs/fastqc/SRR7058339_1_raw.fastqc.err logs/fastqc/SRR7058339_2_raw.fastqc.err logs/fastqc/SRR7058333_1_raw.fastqc.err logs/fastqc/SRR7058333_2_raw.fastqc.err ' returned non-zero exit status 137. File "/sfs/lustre/scratch/mk9uc/RNA_Seq/Snakefile", line 11, in __rule_fastqc_raw File "/apps/software/standard/core/anaconda/5.2.0-py3.6/lib/python3.6/concurrent/futures/thread.py", line 56, in run Removing output files of failed job fastqc_raw since they might be corrupted:
