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test/benchmark/results/caller_comparison_igenvar_only-runtime.md
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# 2022-03-30 | ||
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## L1 | ||
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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 | ||
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## L2 | ||
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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 | ||
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## L3 | ||
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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 | ||
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## S1 | ||
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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 | ||
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## S2 | ||
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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 | ||
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## S1L1 | ||
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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 | ||
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## S1L2 | ||
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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 | ||
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## S1L3 | ||
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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 | ||
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## S2L1 | ||
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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 | ||
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## S2L2 | ||
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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 | ||
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## S2L3 | ||
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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 |