#!/bin/sh
#PBS -l mem=10gb
#PBS -l nodes=1:ppn=10
#PBS -l walltime=02:00:00
#PBS -N JOBNAME.bowtie2_alignReads.cell=HMG021,treat=repl1,chip=Input,reps=rep1
#PBS -o logs/bowtie2_alignReads.cell=HMG021,treat=repl1,chip=Input,reps=rep1.out

#PBS -e logs/bowtie2_alignReads.cell=HMG021,treat=repl1,chip=Input,reps=rep1.err
rams": {"index": "/home/hd/hd_hd/hd_ow424/assemblies/Homo_sapiens/GRCh38/Bowtie2Index/genome", "algnpara": "--sensitive -q -p 10", "prefix": "/beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/HMG021/repl1/Input/bam/HMG021_repl1_Input_rep1_mkdup_sorted", "bamdir": "/beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/HMG021/repl1/Input/bam/"}, "log": [], "threads": 1, "resources": {}, "jobid": 17, "cluster": {"walltime": "02:00:00", "cores": 10, "memory": "10gb", "queue": "single", "name": "JOBNAME.bowtie2_alignReads.cell=HMG021,treat=repl1,chip=Input,reps=rep1", "output": "logs/bowtie2_alignReads.cell=HMG021,treat=repl1,chip=Input,reps=rep1.out", "error": "logs/bowtie2_alignReads.cell=HMG021,treat=repl1,chip=Input,reps=rep1.err"}}
cd /beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/pipelines-chipseq && \
/home/hd/hd_hd/hd_ow424/miniconda3/envs/snakemake/bin/python -m snakemake /beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/HMG021/repl1/Input/bam/HMG021_repl1_Input_rep1.bam /beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/HMG021/repl1/Input/bam/HMG021_repl1_Input_rep1.tmp.bam /beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/HMG021/repl1/Input/bam/HMG021_repl1_Input_rep1.tmp.mate.bam /beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/HMG021/repl1/Input/bam/HMG021_repl1_Input_rep1.name.sort.tmp.bam /beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/HMG021/repl1/Input/bam/HMG021_repl1_Input_rep1_mkdup_sorted.bam /beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/HMG021/repl1/Input/QC/HMG021_repl1_Input_rep1_bowtie2.log /beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/HMG021/repl1/Input/QC/HMG021_repl1_Input_rep1_flagstats.txt --snakefile /beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/pipelines-chipseq/Snakefile \
--force -j --keep-target-files --keep-shadow --keep-remote \
--wait-for-files /beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/pipelines-chipseq/.snakemake/tmp.tvanhs4z /beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/HMG021/repl1/Input/fastq_trimmed/HMG021_repl1_Input_rep1_trimmed.fq.gz /beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/pipelines-chipseq/envs/e869039e --latency-wait 50 \
--benchmark-repeats 1 \
\
--force-use-threads --wrapper-prefix https://bitbucket.org/snakemake/snakemake-wrappers/raw/ \
   --nocolor \
--notemp --quiet --no-hooks --nolock --use-conda  --conda-prefix /beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/pipelines-chipseq/envs  --force-use-threads  --allowed-rules bowtie2_alignReads  && touch "/beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/pipelines-chipseq/.snakemake/tmp.tvanhs4z/17.jobfinished" || (touch "/beegfs/work/ws/hd_ow424-chipseqtest-0/chipseq/pipelines-chipseq/.snakemake/tmp.tvanhs4z/17.jobfailed"; exit 1)