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work_log_run_pecgsb1
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 1
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 2
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 3
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 4
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 5
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 6
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 7
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 8
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.mm.tsv --users songcao --groupname SomaticWXS --step 9
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.chol.tsv --users songcao --groupname SomaticWXS --step 9
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 9
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.mm.tsv --users songcao --groupname SomaticWXS --step 10
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.chol.tsv --users songcao --groupname SomaticWXS --step 10
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 10
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.mm.tsv --users songcao --groupname SomaticWXS --step 11
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.chol.tsv --users songcao --groupname SomaticWXS --step 11
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 11
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.mm.tsv --users songcao --groupname SomaticWXS --step 12
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.chol.tsv --users songcao --groupname SomaticWXS --step 12
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 12
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.mm.tsv --users songcao --groupname SomaticWXS --step 13
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.chol.tsv --users songcao --groupname SomaticWXS --step 13
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 13
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 1 --sre 1
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 2 --sre 1
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 3 --sre 1
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 4 --sre 1
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail --log /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 1
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail --log /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 2
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail --log /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 3
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail --log /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 4
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail --log /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 5
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail --log /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 6
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail --log /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 7
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail --log /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 8
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail --log /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 9
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail --log /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 10
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail --log /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 11
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail --log /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 12
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail --log /storage1/fs1/dinglab/Active/Projects/scao/pecgsb1/MMfail.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 13
## step 12
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.mm.tsv --users songcao --groupname SomaticWXS --step 12
##step 13
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.mm.tsv --users songcao --groupname SomaticWXS --step 13
## run by using v2.2
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgs/MMadd --log /storage1/fs1/dinglab/Active/Projects/scao/pecgs/MMadd.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.mm.tsv --users songcao --groupname SomaticWXS --step 11 --sre 1
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/pecgs/MMadd --log /storage1/fs1/dinglab/Active/Projects/scao/pecgs/MMadd.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.mm.tsv --users songcao --groupname SomaticWXS --step 12 --sre 1