time /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//delly_v0.7.3_cga2_160428_static_openmpi call -t TRA -o translocations.vcf -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/sim_wnormal_10x_d1.rh.bam /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.bam
[2016-Aug-26 21:04:29] delly call -t TRA -x /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//human.hg19.excl.tsv -o translocations.bcf -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/sim_wnormal_10x_d1.rh.bam /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.bam 
[2016-Aug-26 21:05:10] Paired-end clustering

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-26 22:14:34] Split-read alignment

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-28 01:23:48] Junction read annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-28 02:17:22] Breakpoint spanning coverage annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-28 20:36:20] Genotyping

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-28 20:41:00] Library statistics
Sample: normfull_0.6_subsampled
RG: ID=id,Median=338,MAD=20,LibLayout=2,MaxSizeCut=518,MinSizeCut=158,UniqueDiscordantPairs=4388030
Sample: sim_wnormal_10x_d1.rh
RG: ID=tumor-,Median=339,MAD=21,LibLayout=2,MaxSizeCut=528,MinSizeCut=150,UniqueDiscordantPairs=2258594
[2016-Aug-28 20:41:00] Done.
time /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//delly_v0.7.3_cga2_160428_static_openmpi filter -t TRA -f somatic -o translocations.somatic.bcf -s samples.tsv -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta translocations.bcf
[2016-Aug-28 20:41:03] delly filter -t TRA -f somatic -o translocations.somatic.bcf -s samples.tsv -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta translocations.bcf 
[2016-Aug-28 20:41:03] Filtering VCF/BCF file

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-28 20:41:13] Done.
time /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//delly_v0.7.3_cga2_160428_static_openmpi call -t INV -x /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//human.hg19.excl.tsv -o inversions.bcf -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/sim_wnormal_10x_d1.rh.bam /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.bam
[2016-Aug-28 20:41:13] delly call -t INV -x /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//human.hg19.excl.tsv -o inversions.bcf -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/sim_wnormal_10x_d1.rh.bam /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.bam 
[2016-Aug-28 20:41:36] Paired-end clustering

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-28 21:38:21] Split-read alignment

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-29 00:31:04] Junction read annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-29 00:37:46] Breakpoint spanning coverage annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-29 02:43:03] Read-depth annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-29 05:54:18] Genotyping

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-29 05:54:47] Library statistics
Sample: normfull_0.6_subsampled
RG: ID=id,Median=338,MAD=20,LibLayout=2,MaxSizeCut=518,MinSizeCut=158,UniqueDiscordantPairs=283107
Sample: sim_wnormal_10x_d1.rh
RG: ID=tumor-,Median=339,MAD=21,LibLayout=2,MaxSizeCut=528,MinSizeCut=150,UniqueDiscordantPairs=144327
[2016-Aug-29 05:54:47] Done.
time /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//delly_v0.7.3_cga2_160428_static_openmpi filter -t INV -f somatic -o inversions.somatic.bcf -s samples.tsv -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta inversions.bcf
[2016-Aug-29 05:54:47] delly filter -t INV -f somatic -o inversions.somatic.bcf -s samples.tsv -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta inversions.bcf 
[2016-Aug-29 05:54:47] Filtering VCF/BCF file

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-29 05:55:00] Done.
time /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//delly_v0.7.3_cga2_160428_static_openmpi call -t DUP -x /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//human.hg19.excl.tsv -o duplications.bcf -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/sim_wnormal_10x_d1.rh.bam /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.bam
[2016-Aug-29 05:55:00] delly call -t DUP -x /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//human.hg19.excl.tsv -o duplications.bcf -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/sim_wnormal_10x_d1.rh.bam /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.bam 
[2016-Aug-29 05:55:28] Paired-end clustering

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-29 06:48:38] Split-read alignment

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-29 09:45:29] Junction read annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-29 09:53:43] Breakpoint spanning coverage annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-29 11:58:47] Read-depth annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-29 16:10:53] Genotyping

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-29 16:11:22] Library statistics
Sample: normfull_0.6_subsampled
RG: ID=id,Median=338,MAD=20,LibLayout=2,MaxSizeCut=518,MinSizeCut=158,UniqueDiscordantPairs=311701
Sample: sim_wnormal_10x_d1.rh
RG: ID=tumor-,Median=339,MAD=21,LibLayout=2,MaxSizeCut=528,MinSizeCut=150,UniqueDiscordantPairs=180421
[2016-Aug-29 16:11:22] Done.
time /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//delly_v0.7.3_cga2_160428_static_openmpi filter -t DUP -f somatic -o duplications.somatic.bcf -s samples.tsv -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta duplications.bcf
[2016-Aug-29 16:11:23] delly filter -t DUP -f somatic -o duplications.somatic.bcf -s samples.tsv -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta duplications.bcf 
[2016-Aug-29 16:11:23] Filtering VCF/BCF file

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-29 16:11:31] Done.
time /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//delly_v0.7.3_cga2_160428_static_openmpi call -t DEL -x /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//human.hg19.excl.tsv -o deletions.bcf -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/sim_wnormal_10x_d1.rh.bam /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.bam
[2016-Aug-29 16:11:31] delly call -t DEL -x /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//human.hg19.excl.tsv -o deletions.bcf -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/sim_wnormal_10x_d1.rh.bam /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.bam 
[2016-Aug-29 16:12:00] Paired-end clustering

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-30 02:59:47] Split-read alignment

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-30 11:56:58] Junction read annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-30 12:23:53] Breakpoint spanning coverage annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-30 15:16:56] Read-depth annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-30 22:29:25] Genotyping

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-30 22:43:16] Library statistics
Sample: normfull_0.6_subsampled
RG: ID=id,Median=338,MAD=20,LibLayout=2,MaxSizeCut=518,MinSizeCut=158,UniqueDiscordantPairs=5106093
Sample: sim_wnormal_10x_d1.rh
RG: ID=tumor-,Median=339,MAD=21,LibLayout=2,MaxSizeCut=528,MinSizeCut=150,UniqueDiscordantPairs=2779790
[2016-Aug-30 22:43:16] Done.
time /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/DELLY/broadinstitute.org/cancer.genome.analysis/10850/48//delly_v0.7.3_cga2_160428_static_openmpi filter -t DEL -f somatic -o deletions.somatic.bcf -s samples.tsv -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta deletions.bcf
[2016-Aug-30 22:43:17] delly filter -t DEL -f somatic -o deletions.somatic.bcf -s samples.tsv -g /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta deletions.bcf 
[2016-Aug-30 22:43:17] Filtering VCF/BCF file

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2016-Aug-30 22:43:23] Done.
all files: translocations.vcf inversions.vcf duplications.vcf deletions.vcf
Somatic files:  translocations.somatic.vcf inversions.somatic.vcf duplications.somatic.vcf deletions.somatic.vcf
4
4