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NYU CGSB Genomics Core Facility
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NYUAD 131008_SN7001341_0056_AD2B1HACXX #132

Closed smondet closed 10 years ago

smondet commented 10 years ago
smondet commented 10 years ago 
 $ qsub -v DIR=131008_SN7001341_0056_AD2B1HACXX ~/bin/rsync-tar.pbs 
972489.hpc0.abudhabi.nyu.edu
PBS Job Id: 972489.hpc0.abudhabi.nyu.edu
Job Name:   tar-hiseq-rsync
Exec host:  compute-1-22/9
Execution terminated
Exit_status=0
resources_used.cput=00:58:17
resources_used.mem=14020kb
resources_used.vmem=342300kb
resources_used.walltime=04:38:58
smondet commented 10 years ago

on ADHS:

[sm4431@ADUAE119-LAP archive]$ nohup ./do_md5.sh 131008_SN7001341_0056_AD2B1HACXX.tar.gz &
[sm4431@ADUAE119-LAP archive]$ cat 2013-10-18.19\:12\:00.do_md5.out 
MD5 done: ret: 0
[sm4431@ADUAE119-LAP archive]$ cat 2013-10-18.19\:12\:00.131008_SN7001341_0056_AD2B1HACXX.tar.gz.md5 
e23def554fd6fa9ecbc6e180b4258186  131008_SN7001341_0056_AD2B1HACXX.tar.gz
smondet commented 10 years ago 
gencore@butinah-0-4:~/bin $ qsub -v DIR=131008_SN7001341_0056_AD2B1HACXX untar.pbs 
973728.hpc0.abudhabi.nyu.edu

PBS Job Id: 973728.hpc0.abudhabi.nyu.edu
Job Name:   untar_hiseq_raw
Exec host:  compute-2-30/4
Execution terminated
Exit_status=0
resources_used.cput=01:13:08
resources_used.mem=4756kb
resources_used.vmem=345212kb
resources_used.walltime=05:59:06
smondet commented 10 years ago 
$ qsub -v DIR=131008_SN7001341_0056_AD2B1HACXX cp-to-archive.pbs 
977345.hpc0.abudhabi.nyu.edu

PBS Job Id: 977345.hpc0.abudhabi.nyu.edu
Job Name:   archive-tar
Exec host:  compute-3-24/10
Execution terminated
Exit_status=0
resources_used.cput=00:03:53
resources_used.mem=5804kb
resources_used.vmem=330072kb
resources_used.walltime=00:45:47
smondet commented 10 years ago 
gencore@butinah-0-3:/data/cgsb/gencore/bcl_to_fastq/131008_SN7001341_0056_AD2B1HACXX $ scp -P 4410  sm4431@192.168.233.124:"/share/Sample\ Sheets/56_D2B1HACXX.csv" .
smondet commented 10 years ago 
gencore@butinah-0-3:/data/cgsb/gencore/bcl_to_fastq/131008_SN7001341_0056_AD2B1HACXX $ cat pbs/script.pbs                                                                                                                                                       
#!/bin/bash
#PBS -m abe
#PBS -M sm4431@nyu.edu
#PBS -V
#PBS -o /data/cgsb/gencore/bcl_to_fastq/131008_SN7001341_0056_AD2B1HACXX/pbs/out$PBS_JOBID.$PBS_JOBNAME.stdout
#PBS -e /data/cgsb/gencore/bcl_to_fastq/131008_SN7001341_0056_AD2B1HACXX/pbs/err$PBS_JOBID.$PBS_JOBNAME.stderr
#PBS -l nodes=1:ppn=12,walltime=48:00:00
#PBS -N bcl_to_fastq-56

module load bcl2fastq/gnu/1.8.4

IN_ROOT=/scratch/gencore/
OUT_ROOT=/data/cgsb/gencore/bcl_to_fastq
RUN=131008_SN7001341_0056_AD2B1HACXX

configureBclToFastq.pl \
  --fastq-cluster-count 800000000 \
  --input-dir $IN_ROOT/$RUN/Data/Intensities/BaseCalls \
  --output-dir $OUT_ROOT/$RUN/Unaligned \
  --sample-sheet $OUT_ROOT/$RUN/SampleSheet.csv \
  --use-bases-mask Y*,I8,I8,Y* \
  --mismatches 1
ret_config=$?
if [ $ret_config -ne 0 ]; then
        echo "CONFIGURE FAILED: $ret_config"
        exit $ret_config
fi

cd $OUT_ROOT/$RUN/Unaligned
make -j 12
gencore@butinah-0-3:/data/cgsb/gencore/bcl_to_fastq/131008_SN7001341_0056_AD2B1HACXX $ cat SampleSheet.csv 
FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject
D2B1HACXX,1,MJH,,TCCTGAGC-TATCCTCT,,N,,,Lane1
D2B1HACXX,1,CHI,,AGGCAGAA-AGAGTAGA,,N,,,Lane1
D2B1HACXX,2,Tunisian1,,TAAGGCGA-TAGATCGC,,N,,,Lane2
D2B1HACXX,2,Tunisian2,,CGTACTAG-CTCTCTAT,,N,,,Lane2
D2B1HACXX,3,DBS,,TCCTGAGC-TATCCTCT,,N,,,Lane3
D2B1HACXX,3,PakE,,CGTACTAG-TAGATCGC,,N,,,Lane3
D2B1HACXX,5,MKT,,AGGCAGAA-AGAGTAGA,,N,,,Lane5
D2B1HACXX,5,PakP,,TCCTGAGC-TATCCTCT,,N,,,Lane5
D2B1HACXX,6,Iranian2,,TCCTGAGC-TATCCTCT,,N,,,Lane6
D2B1HACXX,6,Iranian4,,AGGCAGAA-AGAGTAGA,,N,,,Lane6
D2B1HACXX,7,HELWA,,TCCTGAGC-TATCCTCT,,N,,,Lane7
D2B1HACXX,7,HIL,,AGGCAGAA-AGAGTAGA,,N,,,Lane7
D2B1HACXX,8,HIRI,,TCCTGAGC-TATCCTCT,,N,,,Lane8
D2B1HACXX,8,PakF,,TCCTGAGC-AGAGTAGA,,N,,,Lane8
gencore@butinah-0-3:/data/cgsb/gencore/bcl_to_fastq/131008_SN7001341_0056_AD2B1HACXX $ qsub pbs/script.pbs 
977598.hpc0.abudhabi.nyu.edu

PBS Job Id: 977598.hpc0.abudhabi.nyu.edu
Job Name:   bcl_to_fastq-56
Exec host:  compute-1-22/11+compute-1-22/10+compute-1-22/9+compute-1-22/8+compute-1-22/7+compute-1-22/6+compute-1-22/5+compute-1-22/4+compute-1-22/3+compute-1-22/2+compute-1-22/1+compute-1-22/0
Execution terminated
Exit_status=0
resources_used.cput=06:56:00
resources_used.mem=363712kb
resources_used.vmem=7517264kb
resources_used.walltime=06:10:35
smondet commented 10 years ago

Lane 8 with 1 index:

PBS Job Id: 985938.hpc0.abudhabi.nyu.edu
Job Name:   bcl_to_fastq-56
Exec host:  compute-1-14/11+compute-1-14/10+compute-1-14/9+compute-1-14/8+compute-1-14/7+compute-1-14/6+compute-1-14/5+compute-1-14/4+compute-1-14/3+compute-1-14/2+compute-1-14/1+compute-1-14/0
Execution terminated
Exit_status=0
resources_used.cput=01:11:15
resources_used.mem=183504kb
resources_used.vmem=6397908kb
resources_used.walltime=00:33:30