-
Notifications
You must be signed in to change notification settings - Fork 7
/
work_log_run_confirmatory_gbm_b1
59 lines (30 loc) · 10.4 KB
/
work_log_run_confirmatory_gbm_b1
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
## b1 batch ##
mkdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 1
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 2
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 3
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 4
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 5
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 6
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 7
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 8
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 9
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 10
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 11
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 12
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 13
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 14
## b2 batch
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 1
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 2
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 3
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 4
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 5
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 6
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 7
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 8
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 9
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 10
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 11
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 12
perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 13