-
Notifications
You must be signed in to change notification settings - Fork 7
/
work_log_run_ctspkirc
59 lines (29 loc) · 10.8 KB
/
work_log_run_ctspkirc
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
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 1
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 2
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 3
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 4
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 5
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 6 --sre 1
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 7
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 8
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 9
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 10
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 11
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 12
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 13
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 3
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 3
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 8
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 9
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 10
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 11
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 12
perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 13
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 8
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 5
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 7
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 9
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 10
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 11
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 12
perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/ctspkirc --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/ctspkirc.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/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 13