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[DOC] Add results
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Signed-off-by: Lydia Buntrock <[email protected]>
Irallia committed Apr 12, 2022
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# 2022-03-30

## L1

Done with clustering. Found 8696029 junction clusters.
No refinement was selected.
Detected 4805290 SVs.
Command being timed: `./build/iGenVar/bin/iGenVar --input_long_reads data/long_reads/HG002_PacBio_GRCh38.bam --output results/caller_comparison_iGenVar_only/L1/variants.vcf --vcf_sample_name HG002 --threads 2 --verbose --min_var_length 40 --max_var_length 1000000 --min_qual 1`
User time (seconds): 9903.34
System time (seconds): 3953.40
Percent of CPU this job got: 171%
Elapsed (wall clock) time (h:mm:ss or m:ss): 2:14:21
Maximum resident set size (kbytes): 18630536
Major (requiring I/O) page faults: 4364
Minor (reclaiming a frame) page faults: 30171400
Voluntary context switches: 385116
Involuntary context switches: 1276546668
Swaps: 0
File system inputs: 194623416
File system outputs: 6193096


## L2

Done with clustering. Found 67693 junction clusters.
No refinement was selected.
Detected 67693 SVs.
Command being timed: `./build/iGenVar/bin/iGenVar --input_long_reads data/long_reads/HG002.Sequel.10kb.pbmm2.hs37d5.whatshap.haplotag.RTG.10x.trio.bam --output results/caller_comparison_iGenVar_only/L2/variants.vcf --vcf_sample_name HG002 --threads 2 --verbose --min_var_length 40 --max_var_length 1000000 --min_qual 1`
User time (seconds): 2894.02
System time (seconds): 782.43
Percent of CPU this job got: 156%
Elapsed (wall clock) time (h:mm:ss or m:ss): 39:14.92
Maximum resident set size (kbytes): 760840
Major (requiring I/O) page faults: 2
Minor (reclaiming a frame) page faults: 483754
Voluntary context switches: 230340
Involuntary context switches: 282670339
Swaps: 0
File system inputs: 121766248
File system outputs: 1293312

## L3

Done with clustering. Found 6314105 junction clusters.
No refinement was selected.
Detected 368354 SVs.
Command being timed: `./build/iGenVar/bin/iGenVar --input_long_reads data/long_reads/NA24385_phased_possorted_bam.bam --output results/caller_comparison_iGenVar_only/L3/variants.vcf --vcf_sample_name HG002 --threads 2 --verbose --min_var_length 40 --max_var_length 1000000 --min_qual 1`
User time (seconds): 15293.00
System time (seconds): 8260.35
Percent of CPU this job got: 204%
Elapsed (wall clock) time (h:mm:ss or m:ss): 3:12:03
Maximum resident set size (kbytes): 3489880
Major (requiring I/O) page faults: 7113
Minor (reclaiming a frame) page faults: 3178988
Voluntary context switches: 191910
Involuntary context switches: 1901718237
Swaps: 0
File system inputs: 105495784
File system outputs: 95754136

## S1

Done with clustering. Found 26972 junction clusters.
No refinement was selected.
Detected 26972 SVs.
Command being timed: `./build/iGenVar/bin/iGenVar --input_short_reads data/short_reads/HG002.GRCh38.2x250.sorted.bam --output results/caller_comparison_iGenVar_only/S1/variants.vcf --vcf_sample_name HG002 --threads 2 --verbose --min_var_length 40 --max_var_length 1000000 --min_qual 1`
User time (seconds): 33190.72
System time (seconds): 18981.07
Percent of CPU this job got: 318%
Elapsed (wall clock) time (h:mm:ss or m:ss): 4:32:43
Maximum resident set size (kbytes): 3444888
Major (requiring I/O) page faults: 253
Minor (reclaiming a frame) page faults: 33238952
Voluntary context switches: 435998
Involuntary context switches: 2110493527
Swaps: 0
File system inputs: 183434360
File system outputs: 171364800

## S2

Done with clustering. Found 1158118 junction clusters.
No refinement was selected.
Detected 7952 SVs.
Command being timed: `./build/iGenVar/bin/iGenVar --input_short_reads data/short_reads/HG002.mate_pair.sorted.bam --output results/caller_comparison_iGenVar_only/S2/variants.vcf --vcf_sample_name HG002 --threads 2 --verbose --min_var_length 40 --max_var_length 1000000 --min_qual 1`
User time (seconds): 13010.99
System time (seconds): 8528.86
Percent of CPU this job got: 297%
Elapsed (wall clock) time (h:mm:ss or m:ss): 2:00:45
Maximum resident set size (kbytes): 3423272
Major (requiring I/O) page faults: 22
Minor (reclaiming a frame) page faults: 4121719
Voluntary context switches: 13219
Involuntary context switches: 1817142227
Swaps: 0
File system inputs: 109176
File system outputs: 85451624

## S1L1

Done with clustering. Found 8706117 junction clusters.
No refinement was selected.
Detected 4815605 SVs.
Command being timed: `./build/iGenVar/bin/iGenVar --input_short_reads data/short_reads/HG002.GRCh38.2x250.sorted.bam --input_long_reads data/long_reads/HG002_PacBio_GRCh38.bam --output results/caller_comparison_iGenVar_only/S1L1/variants.vcf --vcf_sample_name HG002 --threads 2 --verbose --min_var_length 40 --max_var_length 1000000 --min_qual 1`
User time (seconds): 39950.43
System time (seconds): 20396.18
Percent of CPU this job got: 297%
Elapsed (wall clock) time (h:mm:ss or m:ss): 5:38:30
Maximum resident set size (kbytes): 18692660
Major (requiring I/O) page faults: 3946
Minor (reclaiming a frame) page faults: 42608867
Voluntary context switches: 601877
Involuntary context switches: 3194666817
Swaps: 0
File system inputs: 236568664
File system outputs: 177657464

## S1L2

Done with clustering. Found 94087 junction clusters.
No refinement was selected.
Detected 94087 SVs.
Command being timed: `./build/iGenVar/bin/iGenVar --input_short_reads data/short_reads/HG002.GRCh38.2x250.sorted.bam --input_long_reads data/long_reads/HG002.Sequel.10kb.pbmm2.hs37d5.whatshap.haplotag.RTG.10x.trio.bam --output results/caller_comparison_iGenVar_only/S1L2/variants.vcf --vcf_sample_name HG002 --threads 2 --verbose --min_var_length 40 --max_var_length 1000000 --min_qual 1`
User time (seconds): 36232.29
System time (seconds): 19468.18
Percent of CPU this job got: 313%
Elapsed (wall clock) time (h:mm:ss or m:ss): 4:56:15
Maximum resident set size (kbytes): 3443264
Major (requiring I/O) page faults: 3222
Minor (reclaiming a frame) page faults: 27203688
Voluntary context switches: 476612
Involuntary context switches: 2280543021
Swaps: 0
File system inputs: 173979736
File system outputs: 172898776

## S1L3

Done with clustering. Found 6340858 junction clusters.
No refinement was selected.
Detected 395105 SVs.
Command being timed: `./build/iGenVar/bin/iGenVar --input_short_reads data/short_reads/HG002.GRCh38.2x250.sorted.bam --input_long_reads data/long_reads/NA24385_phased_possorted_bam.bam --output results/caller_comparison_iGenVar_only/S1L3/variants.vcf --vcf_sample_name HG002 --threads 2 --verbose --min_var_length 40 --max_var_length 1000000 --min_qual 1`
User time (seconds): 43819.83
System time (seconds): 22945.57
Percent of CPU this job got: 308%
Elapsed (wall clock) time (h:mm:ss or m:ss): 6:00:41
Maximum resident set size (kbytes): 3563924
Major (requiring I/O) page faults: 3279
Minor (reclaiming a frame) page faults: 26824260
Voluntary context switches: 387882
Involuntary context switches: 2566452379
Swaps: 0
File system inputs: 154989096
File system outputs: 267312320

## S2L1

Done with clustering. Found 9852431 junction clusters.
No refinement was selected.
Detected 4812755 SVs.
Command being timed: `./build/iGenVar/bin/iGenVar --input_short_reads data/short_reads/HG002.mate_pair.sorted.bam --input_long_reads data/long_reads/HG002_PacBio_GRCh38.bam --output results/caller_comparison_iGenVar_only/S2L1/variants.vcf --vcf_sample_name HG002 --threads 2 --verbose --min_var_length 40 --max_var_length 1000000 --min_qual 1`
User time (seconds): 22226.71
System time (seconds): 12079.06
Percent of CPU this job got: 233%
Elapsed (wall clock) time (h:mm:ss or m:ss): 4:04:22
Maximum resident set size (kbytes): 19085596
Major (requiring I/O) page faults: 160
Minor (reclaiming a frame) page faults: 24354133
Voluntary context switches: 418630
Involuntary context switches: 2713660822
Swaps: 0
File system inputs: 194667000
File system outputs: 91499152

## S2L2

Done with clustering. Found 1224088 junction clusters.
No refinement was selected.
Detected 73938 SVs.
Command being timed: `./build/iGenVar/bin/iGenVar --input_short_reads data/short_reads/HG002.mate_pair.sorted.bam --input_long_reads data/long_reads/HG002.Sequel.10kb.pbmm2.hs37d5.whatshap.haplotag.RTG.10x.trio.bam --output results/caller_comparison_iGenVar_only/S2L2/variants.vcf --vcf_sample_name HG002 --threads 2 --verbose --min_var_length 40 --max_var_length 1000000 --min_qual 1`
User time (seconds): 15647.20
System time (seconds): 9037.36
Percent of CPU this job got: 253%
Elapsed (wall clock) time (h:mm:ss or m:ss): 2:42:28
Maximum resident set size (kbytes): 3417652
Major (requiring I/O) page faults: 42
Minor (reclaiming a frame) page faults: 10475699
Voluntary context switches: 389753
Involuntary context switches: 1398807520
Swaps: 0
File system inputs: 192060304
File system outputs: 86744600

## S2L3

Done with clustering. Found 7457031 junction clusters.
No refinement was selected.
Detected 373861 SVs.
Command being timed: `./build/iGenVar/bin/iGenVar --input_short_reads data/short_reads/HG002.mate_pair.sorted.bam --input_long_reads data/long_reads/NA24385_phased_possorted_bam.bam --output results/caller_comparison_iGenVar_only/S2L3/variants.vcf --vcf_sample_name HG002 --threads 2 --verbose --min_var_length 40 --max_var_length 1000000 --min_qual 1`
User time (seconds): 25386.84
System time (seconds): 14474.91
Percent of CPU this job got: 253%
Elapsed (wall clock) time (h:mm:ss or m:ss): 4:21:37
Maximum resident set size (kbytes): 4173960
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 37214
Minor (reclaiming a frame) page faults: 5393501
Voluntary context switches: 234848
Involuntary context switches: 2703304840
Swaps: 0
File system inputs: 104955264
File system outputs: 180960336

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