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work_log_run_alchemist_b1
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work_log_run_alchemist_b1
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perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b0 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b0.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 1
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b0 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b0.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 2 --sre 1
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b0 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b0.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 3
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b0 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b0.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 4
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 1
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 2 --sre 1
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 3
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 4
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 1
## get unfinished j4 jobs running
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 2
## get unfinished j3 jobs running
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j4_unfinished --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j4_unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 4 --sre 1
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 3 --sre 1
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 5
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 6
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 7
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 8
###
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 5
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 6
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 7
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 8
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished_2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished.2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 3 --sre 1
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished_2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished.2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 5 --sre 1
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished_2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished.2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 6 --sre 1
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished_2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished.2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 7 --sre 1
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished_2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished.2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 8 --sre 1
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished_2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/j3_unfinished.2.log --groupname SomaticWXS --users songcao --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 9
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 9
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 10
#perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 11
#perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 12
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --groupname SomaticWXS --users songcao --step 12
perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --groupname SomaticWXS --users songcao --step 13
#perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --step 13