Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/e814414c63d0258e57b3010ee1fa05/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/22717aa6154d7d4755ff63daccf675/NA12878_c_0002_gDNA_0004_B23KGCJLT4_1/NA12878_c_0002_gDNA_0004_B23KGCJLT4_1_R1.fastq.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/e814414c63d0258e57b3010ee1fa05/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/22717aa6154d7d4755ff63daccf675/NA12878_c_0002_gDNA_0004_B23KGCJLT4_1/NA12878_c_0002_gDNA_0004_B23KGCJLT4_1_R2.fastq.gz
==> STAGING COMPLETE (7 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o NA12878_c_0002_gDNA_0004_B23KGCJLT4_1.bam --sam2bam -
This software is licensed to bgold@natera.com by Sentieon Inc.
This software is licensed to bgold@natera.com by Sentieon Inc.
version: sentieon-genomics-202308.03
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
[M::main_mem] bwa index loaded in 1740.117 CPU sec, 62.970 real sec
[M::process] read 684202 sequences (100000144 bp) in 1.149 CPU sec, 1.156 real sec...
[M::process] read 682766 sequences (100000236 bp) in 1.714 CPU sec, 1.723 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 284745, 1, 15)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 305, 423)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 865)
[M::mem_pestat] mean and std.dev: (322.82, 152.86)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1086)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (176, 183, 313)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 587)
[M::mem_pestat] mean and std.dev: (207.07, 72.45)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 724)
[M::mem_pestat] skip orientation RR
[M::process] read 682260 sequences (100000051 bp) in 1.687 CPU sec, 1.704 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 283980, 0, 7)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (208, 313, 434)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 886)
[M::mem_pestat] mean and std.dev: (330.62, 155.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1112)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 684202 reads in 151.669 CPU sec, 4.782 real sec
[M::process] read 683252 sequences (100000257 bp) in 1.789 CPU sec, 1.842 real sec...
[M::mem_process_seqs] Processed 682766 reads in 103.183 CPU sec, 3.267 real sec
sorting block 0, #reads = 1072372 mem = 536878968 peak = 599478272
[M::process] read 683818 sequences (100000155 bp) in 2.106 CPU sec, 2.150 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 283530, 2, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (209, 315, 437)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 893)
[M::mem_pestat] mean and std.dev: (332.42, 156.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1121)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 683744 sequences (100000159 bp) in 1.813 CPU sec, 1.825 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 284095, 3, 8)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 301, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 861)
[M::mem_pestat] mean and std.dev: (321.78, 154.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1081)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (19, 284853, 1, 12)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (172, 197, 305)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 571)
[M::mem_pestat] mean and std.dev: (210.05, 68.35)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 704)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (204, 305, 428)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 876)
[M::mem_pestat] mean and std.dev: (325.54, 154.81)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1100)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (130, 280, 670)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1750)
[M::mem_pestat] mean and std.dev: (373.83, 361.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2290)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 682260 reads in 231.085 CPU sec, 7.377 real sec
[M::mem_process_seqs] Processed 683818 reads in 178.860 CPU sec, 5.742 real sec
sorting block 1, #reads = 1070926 mem = 536880165 peak = 728453120
[M::mem_process_seqs] Processed 683252 reads in 197.719 CPU sec, 6.353 real sec
[M::process] read 683256 sequences (100000233 bp) in 2.265 CPU sec, 2.366 real sec...
sorting block 2, #reads = 1071268 mem = 536879167 peak = 830271488
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 284599, 4, 7)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 301, 422)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 864)
[M::mem_pestat] mean and std.dev: (322.15, 154.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1085)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 684152 sequences (100000002 bp) in 1.931 CPU sec, 1.935 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 284329, 3, 10)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 305, 430)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 884)
[M::mem_pestat] mean and std.dev: (327.16, 157.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1111)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (134, 191, 336)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 740)
[M::mem_pestat] mean and std.dev: (220.30, 104.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 942)
[M::mem_pestat] skip orientation RR
[M::process] read 682700 sequences (100000168 bp) in 1.397 CPU sec, 1.413 real sec...
[M::mem_process_seqs] Processed 683744 reads in 166.653 CPU sec, 5.277 real sec
[M::mem_process_seqs] Processed 683256 reads in 110.068 CPU sec, 3.475 real sec
sorting block 3, #reads = 1072022 mem = 536879524 peak = 830271488
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 284058, 3, 5)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (114, 144, 167)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (8, 273)
[M::mem_pestat] mean and std.dev: (141.22, 39.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 326)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 306, 427)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 877)
[M::mem_pestat] mean and std.dev: (324.31, 153.93)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1102)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::process] read 681914 sequences (100000277 bp) in 2.484 CPU sec, 2.552 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (13, 283809, 2, 2)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (139, 205, 268)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 526)
[M::mem_pestat] mean and std.dev: (183.08, 59.45)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 655)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (209, 317, 438)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 896)
[M::mem_pestat] mean and std.dev: (333.31, 156.95)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1125)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::process] read 683162 sequences (100000074 bp) in 2.038 CPU sec, 2.039 real sec...
[M::mem_process_seqs] Processed 684152 reads in 161.630 CPU sec, 5.103 real sec
[M::mem_process_seqs] Processed 682700 reads in 106.278 CPU sec, 3.355 real sec
sorting block 4, #reads = 1072424 mem = 536878564 peak = 830271488
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 283204, 0, 6)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (268, 962, 4662)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13450)
[M::mem_pestat] mean and std.dev: (1716.80, 1948.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 17844)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (211, 318, 438)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 892)
[M::mem_pestat] mean and std.dev: (334.05, 155.76)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1119)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::process] read 683484 sequences (100000243 bp) in 2.379 CPU sec, 2.469 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 284596, 0, 8)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (206, 309, 429)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 875)
[M::mem_pestat] mean and std.dev: (326.99, 153.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1098)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 683624 sequences (100000294 bp) in 1.865 CPU sec, 1.862 real sec...
[M::mem_process_seqs] Processed 681914 reads in 162.954 CPU sec, 5.160 real sec
sorting block 5, #reads = 1072294 mem = 536880234 peak = 830271488
[M::process] read 683398 sequences (100000144 bp) in 1.698 CPU sec, 1.700 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 284210, 1, 11)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 304, 426)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 872)
[M::mem_pestat] mean and std.dev: (324.45, 154.59)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1095)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (131, 207, 815)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2183)
[M::mem_pestat] mean and std.dev: (356.00, 345.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2867)
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 683484 reads in 94.482 CPU sec, 3.157 real sec
sorting block 6, #reads = 1071728 mem = 536878496 peak = 838299648
[M::mem_process_seqs] Processed 683162 reads in 227.204 CPU sec, 7.375 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 284053, 1, 5)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (196, 272, 313)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 547)
[M::mem_pestat] mean and std.dev: (220.11, 81.76)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 664)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 302, 425)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 871)
[M::mem_pestat] mean and std.dev: (323.79, 155.72)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1094)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::process] read 684248 sequences (100000166 bp) in 2.453 CPU sec, 2.511 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 284259, 1, 3)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 306, 432)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 890)
[M::mem_pestat] mean and std.dev: (328.01, 158.65)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1119)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 683624 reads in 177.781 CPU sec, 5.636 real sec
[M::mem_process_seqs] Processed 683398 reads in 107.472 CPU sec, 3.375 real sec
[M::process] read 683028 sequences (100000039 bp) in 2.215 CPU sec, 2.239 real sec...
sorting block 7, #reads = 1071977 mem = 536881589 peak = 838299648
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 284147, 0, 7)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 307, 431)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 889)
[M::mem_pestat] mean and std.dev: (326.29, 156.42)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1118)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 682752 sequences (100000214 bp) in 2.439 CPU sec, 2.533 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 283937, 0, 3)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (208, 315, 439)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 901)
[M::mem_pestat] mean and std.dev: (332.37, 156.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1132)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 683344 sequences (100000204 bp) in 2.050 CPU sec, 2.051 real sec...
[M::mem_process_seqs] Processed 684248 reads in 160.601 CPU sec, 5.073 real sec
sorting block 8, #reads = 1071153 mem = 536879690 peak = 910667776
[M::mem_process_seqs] Processed 683028 reads in 106.890 CPU sec, 3.373 real sec
sorting block 9, #reads = 1071530 mem = 536878388 peak = 910667776
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 284004, 0, 7)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (208, 314, 436)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 892)
[M::mem_pestat] mean and std.dev: (331.39, 155.65)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1120)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 682766 sequences (100000210 bp) in 2.527 CPU sec, 2.576 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 284493, 0, 10)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (188, 450, 450)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 974)
[M::mem_pestat] mean and std.dev: (328.10, 161.74)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1236)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (205, 308, 430)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 880)
[M::mem_pestat] mean and std.dev: (326.69, 155.09)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1105)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (150, 208, 238)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 414)
[M::mem_pestat] mean and std.dev: (221.60, 86.45)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 567)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 682752 reads in 159.843 CPU sec, 5.049 real sec
[M::process] read 683678 sequences (100000236 bp) in 2.130 CPU sec, 2.131 real sec...
[M::mem_process_seqs] Processed 683344 reads in 108.695 CPU sec, 3.427 real sec
sorting block 10, #reads = 1071123 mem = 536877885 peak = 910667776
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 283934, 1, 12)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (206, 308, 432)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 884)
[M::mem_pestat] mean and std.dev: (328.80, 156.51)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1110)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (171, 194, 272)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 474)
[M::mem_pestat] mean and std.dev: (199.36, 56.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 575)
[M::mem_pestat] skip orientation RR
[M::process] read 683086 sequences (100000274 bp) in 2.491 CPU sec, 2.553 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 284376, 0, 8)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 302, 426)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 876)
[M::mem_pestat] mean and std.dev: (323.96, 156.33)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1101)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 683998 sequences (100000258 bp) in 2.130 CPU sec, 2.127 real sec...
[M::mem_process_seqs] Processed 682766 reads in 160.519 CPU sec, 5.064 real sec
[M::mem_process_seqs] Processed 683678 reads in 107.126 CPU sec, 3.375 real sec
sorting block 11, #reads = 1071221 mem = 536880967 peak = 910667776
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (12, 284011, 2, 2)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (199, 356, 451)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 955)
[M::mem_pestat] mean and std.dev: (333.00, 118.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1207)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (204, 306, 431)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 885)
[M::mem_pestat] mean and std.dev: (327.88, 158.09)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1112)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::process] read 682992 sequences (100000206 bp) in 2.527 CPU sec, 2.595 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 284087, 2, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 305, 432)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 894)
[M::mem_pestat] mean and std.dev: (327.31, 159.15)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1125)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 682654 sequences (100000150 bp) in 1.990 CPU sec, 1.985 real sec...
[M::mem_process_seqs] Processed 683086 reads in 159.943 CPU sec, 5.054 real sec
sorting block 12, #reads = 1071859 mem = 536878738 peak = 910667776
[M::mem_process_seqs] Processed 683998 reads in 101.504 CPU sec, 3.196 real sec
sorting block 13, #reads = 1071303 mem = 536879519 peak = 917053440
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 283607, 3, 7)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (165, 345, 351)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 723)
[M::mem_pestat] mean and std.dev: (243.50, 106.98)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 909)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (206, 311, 434)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 890)
[M::mem_pestat] mean and std.dev: (329.68, 156.55)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1118)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::process] read 682836 sequences (100000039 bp) in 1.944 CPU sec, 1.994 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 284047, 1, 7)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (208, 313, 433)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 883)
[M::mem_pestat] mean and std.dev: (330.00, 154.55)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1108)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 682724 sequences (100000056 bp) in 1.540 CPU sec, 1.542 real sec...
[M::mem_process_seqs] Processed 682992 reads in 128.476 CPU sec, 4.067 real sec
[M::mem_process_seqs] Processed 682654 reads in 84.759 CPU sec, 2.678 real sec
sorting block 14, #reads = 1071334 mem = 536879673 peak = 917053440
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 284324, 1, 15)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (160, 431, 893)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2359)
[M::mem_pestat] mean and std.dev: (431.70, 320.62)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 3092)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (206, 308, 430)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 878)
[M::mem_pestat] mean and std.dev: (327.35, 154.70)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1102)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (148, 176, 260)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 484)
[M::mem_pestat] mean and std.dev: (188.14, 62.47)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 596)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::process] read 683352 sequences (100000235 bp) in 2.475 CPU sec, 2.525 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 284100, 1, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (204, 306, 428)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 876)
[M::mem_pestat] mean and std.dev: (326.51, 155.35)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1100)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 682836 reads in 143.351 CPU sec, 4.536 real sec
[M::mem_process_seqs] Processed 682724 reads in 100.716 CPU sec, 3.161 real sec
[M::process] read 683010 sequences (100000273 bp) in 2.523 CPU sec, 2.552 real sec...
sorting block 15, #reads = 1071077 mem = 536879422 peak = 917053440
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 284189, 1, 9)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 303, 426)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 874)
[M::mem_pestat] mean and std.dev: (324.19, 155.02)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1098)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 684880 sequences (100000207 bp) in 2.715 CPU sec, 2.816 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 283714, 1, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 304, 429)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 881)
[M::mem_pestat] mean and std.dev: (326.43, 156.99)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1107)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 683352 reads in 158.495 CPU sec, 5.033 real sec
[M::mem_process_seqs] Processed 683010 reads in 105.765 CPU sec, 3.325 real sec
sorting block 16, #reads = 1070865 mem = 536878907 peak = 917053440
[M::process] read 684904 sequences (100000274 bp) in 2.499 CPU sec, 2.529 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 284814, 0, 11)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (199, 299, 426)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 880)
[M::mem_pestat] mean and std.dev: (322.69, 157.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1107)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (121, 165, 173)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (17, 277)
[M::mem_pestat] mean and std.dev: (158.45, 48.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 353)
[M::mem_pestat] skip orientation RR
[M::process] read 683376 sequences (100000074 bp) in 2.897 CPU sec, 3.059 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 284602, 0, 6)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (200, 306, 430)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 890)
[M::mem_pestat] mean and std.dev: (324.70, 156.10)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1120)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 684880 reads in 155.141 CPU sec, 4.929 real sec
sorting block 17, #reads = 1071019 mem = 536879590 peak = 917053440
[M::mem_process_seqs] Processed 684904 reads in 100.343 CPU sec, 3.163 real sec
[M::process] read 683956 sequences (100000028 bp) in 2.603 CPU sec, 2.670 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 284391, 1, 7)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (205, 311, 431)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 883)
[M::mem_pestat] mean and std.dev: (327.79, 154.67)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1109)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
sorting block 18, #reads = 1072574 mem = 536879976 peak = 917053440
[M::process] read 684446 sequences (100000099 bp) in 2.535 CPU sec, 2.580 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 284382, 1, 16)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 302, 419)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 853)
[M::mem_pestat] mean and std.dev: (319.96, 150.77)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1070)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (245, 248, 301)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (133, 413)
[M::mem_pestat] mean and std.dev: (247.54, 49.71)
[M::mem_pestat] low and high boundaries for proper pairs: (49, 469)
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 683376 reads in 156.152 CPU sec, 4.952 real sec
[M::mem_process_seqs] Processed 683956 reads in 104.383 CPU sec, 3.283 real sec
[M::process] read 684156 sequences (100000199 bp) in 2.461 CPU sec, 2.500 real sec...
sorting block 19, #reads = 1072045 mem = 536877604 peak = 917053440
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 285200, 3, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (200, 299, 417)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 851)
[M::mem_pestat] mean and std.dev: (318.60, 150.94)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1068)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 683800 sequences (100000286 bp) in 2.518 CPU sec, 2.574 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 284828, 0, 8)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 299, 416)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 846)
[M::mem_pestat] mean and std.dev: (317.48, 149.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1061)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 684446 reads in 158.245 CPU sec, 5.033 real sec
[M::mem_process_seqs] Processed 684156 reads in 105.507 CPU sec, 3.315 real sec
sorting block 20, #reads = 1071799 mem = 536878408 peak = 917053440
[M::process] read 684308 sequences (100000007 bp) in 2.507 CPU sec, 2.542 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 284627, 1, 9)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 297, 411)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 831)
[M::mem_pestat] mean and std.dev: (315.50, 147.82)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1041)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 684376 sequences (100000193 bp) in 2.401 CPU sec, 2.467 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (13, 284714, 3, 9)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (155, 181, 1141)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3113)
[M::mem_pestat] mean and std.dev: (331.92, 363.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4099)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (198, 295, 414)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 846)
[M::mem_pestat] mean and std.dev: (316.47, 151.12)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1062)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::mem_process_seqs] Processed 683800 reads in 160.477 CPU sec, 5.085 real sec
[M::process] read 682956 sequences (100000131 bp) in 2.100 CPU sec, 2.113 real sec...
sorting block 21, #reads = 1072141 mem = 536882379 peak = 917053440
[M::mem_process_seqs] Processed 684308 reads in 107.941 CPU sec, 3.395 real sec
sorting block 22, #reads = 1071054 mem = 536877298 peak = 942047232
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (15, 284851, 0, 8)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (299, 299, 302)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (293, 308)
[M::mem_pestat] mean and std.dev: (300.64, 1.49)
[M::mem_pestat] low and high boundaries for proper pairs: (290, 311)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 304, 424)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 870)
[M::mem_pestat] mean and std.dev: (322.52, 153.38)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1093)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::process] read 683558 sequences (100000184 bp) in 2.598 CPU sec, 2.674 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 284268, 3, 6)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (205, 307, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 853)
[M::mem_pestat] mean and std.dev: (322.66, 149.59)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1069)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 684376 reads in 154.165 CPU sec, 4.885 real sec
[M::process] read 684082 sequences (100000251 bp) in 2.261 CPU sec, 2.267 real sec...
[M::mem_process_seqs] Processed 682956 reads in 101.558 CPU sec, 3.189 real sec
sorting block 23, #reads = 1073039 mem = 536877640 peak = 942047232
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 284797, 0, 7)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 301, 417)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 847)
[M::mem_pestat] mean and std.dev: (318.95, 148.88)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1062)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 683736 sequences (100000107 bp) in 2.537 CPU sec, 2.606 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 284436, 4, 6)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 299, 415)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 843)
[M::mem_pestat] mean and std.dev: (317.35, 148.99)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1057)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 683558 reads in 162.126 CPU sec, 5.143 real sec
[M::process] read 683272 sequences (100000297 bp) in 2.146 CPU sec, 2.149 real sec...
[M::mem_process_seqs] Processed 684082 reads in 109.340 CPU sec, 3.441 real sec
sorting block 24, #reads = 1070750 mem = 536877519 peak = 942047232
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 284543, 2, 13)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 302, 417)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 847)
[M::mem_pestat] mean and std.dev: (319.39, 149.99)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1062)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (132, 153, 218)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[M::mem_pestat] mean and std.dev: (163.75, 50.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[M::mem_pestat] skip orientation RR
[M::process] read 684118 sequences (100000193 bp) in 2.898 CPU sec, 2.981 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 284273, 4, 11)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 303, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 857)
[M::mem_pestat] mean and std.dev: (322.29, 152.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1075)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (150, 236, 241)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 423)
[M::mem_pestat] mean and std.dev: (206.90, 76.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 514)
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 683736 reads in 154.960 CPU sec, 4.893 real sec
[M::mem_process_seqs] Processed 683272 reads in 103.338 CPU sec, 3.250 real sec
[M::process] read 684268 sequences (100000003 bp) in 2.366 CPU sec, 2.391 real sec...
sorting block 25, #reads = 1070261 mem = 536877482 peak = 942047232
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 283985, 0, 9)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (200, 299, 419)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 857)
[M::mem_pestat] mean and std.dev: (319.72, 152.66)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1076)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 683190 sequences (100000261 bp) in 2.410 CPU sec, 2.480 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 284880, 0, 7)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 303, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 861)
[M::mem_pestat] mean and std.dev: (321.27, 152.25)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1081)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 684118 reads in 161.677 CPU sec, 5.120 real sec
sorting block 26, #reads = 1070976 mem = 536885110 peak = 961011712
[M::process] read 684478 sequences (100000104 bp) in 2.176 CPU sec, 2.174 real sec...
[M::mem_process_seqs] Processed 684268 reads in 104.108 CPU sec, 3.273 real sec
sorting block 27, #reads = 1070545 mem = 536880314 peak = 988749824
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 284162, 3, 9)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (206, 307, 424)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 860)
[M::mem_pestat] mean and std.dev: (324.06, 151.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1078)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 684396 sequences (100000245 bp) in 2.612 CPU sec, 2.682 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 284970, 1, 13)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (200, 299, 414)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 842)
[M::mem_pestat] mean and std.dev: (317.32, 149.40)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1056)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (181, 190, 529)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1225)
[M::mem_pestat] mean and std.dev: (276.17, 141.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1573)
[M::mem_pestat] skip orientation RR
[M::process] read 683614 sequences (100000035 bp) in 2.150 CPU sec, 2.151 real sec...
[M::mem_process_seqs] Processed 683190 reads in 174.447 CPU sec, 5.518 real sec
[M::mem_process_seqs] Processed 684478 reads in 127.795 CPU sec, 4.029 real sec
sorting block 28, #reads = 1070581 mem = 536877758 peak = 988749824
[M::process] read 683188 sequences (100000141 bp) in 2.228 CPU sec, 2.301 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 285065, 0, 4)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (200, 298, 415)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 845)
[M::mem_pestat] mean and std.dev: (317.28, 149.62)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1060)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 685018 sequences (100000153 bp) in 1.620 CPU sec, 1.626 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 284870, 1, 8)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 300, 415)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 841)
[M::mem_pestat] mean and std.dev: (318.13, 148.95)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1054)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 284247, 1, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 304, 423)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 863)
[M::mem_pestat] mean and std.dev: (322.73, 152.29)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1083)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 684396 reads in 232.887 CPU sec, 7.424 real sec
[M::mem_process_seqs] Processed 683614 reads in 158.198 CPU sec, 5.069 real sec
sorting block 29, #reads = 1062000 mem = 536879863 peak = 988749824
[M::mem_process_seqs] Processed 683188 reads in 173.895 CPU sec, 5.587 real sec
sorting block 30, #reads = 1067365 mem = 536878438 peak = 988749824
[M::process] read 684194 sequences (100000301 bp) in 2.303 CPU sec, 2.397 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 284389, 4, 8)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (197, 296, 417)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 857)
[M::mem_pestat] mean and std.dev: (317.46, 153.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1077)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 683298 sequences (100000150 bp) in 1.717 CPU sec, 1.752 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 284666, 6, 10)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (208, 253, 355)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 649)
[M::mem_pestat] mean and std.dev: (260.20, 84.47)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 796)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 301, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 861)
[M::mem_pestat] mean and std.dev: (321.19, 152.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1081)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (208, 740, 745)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1819)
[M::mem_pestat] mean and std.dev: (494.30, 262.48)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2356)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 685018 reads in 144.971 CPU sec, 4.604 real sec
[M::mem_process_seqs] Processed 684194 reads in 88.832 CPU sec, 2.792 real sec
sorting block 31, #reads = 1064418 mem = 536880656 peak = 988749824
[M::process] read 683596 sequences (100000016 bp) in 1.920 CPU sec, 1.977 real sec...
[M::process] read 683380 sequences (100000163 bp) in 2.066 CPU sec, 2.135 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 284835, 1, 9)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 303, 420)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 854)
[M::mem_pestat] mean and std.dev: (320.49, 149.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1071)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 683596 reads in 82.760 CPU sec, 2.604 real sec
[M::process] read 682700 sequences (100000055 bp) in 1.810 CPU sec, 1.820 real sec...
sorting block 32, #reads = 1069909 mem = 536879806 peak = 988749824
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 284440, 0, 13)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (204, 304, 418)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 846)
[M::mem_pestat] mean and std.dev: (320.49, 148.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1060)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (160, 278, 278)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 514)
[M::mem_pestat] mean and std.dev: (230.46, 90.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 632)
[M::mem_pestat] skip orientation RR
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 284340, 1, 7)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 304, 425)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 869)
[M::mem_pestat] mean and std.dev: (323.87, 153.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1091)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 683298 reads in 214.683 CPU sec, 6.789 real sec
[M::process] read 682208 sequences (100000085 bp) in 1.716 CPU sec, 1.717 real sec...
[M::mem_process_seqs] Processed 683380 reads in 103.385 CPU sec, 3.272 real sec
sorting block 33, #reads = 1071128 mem = 536881871 peak = 988749824
[M::process] read 403976 sequences (59214828 bp) in 1.398 CPU sec, 1.462 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 284581, 2, 12)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (205, 305, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 853)
[M::mem_pestat] mean and std.dev: (322.47, 149.66)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1069)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (225, 280, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (115, 390)
[M::mem_pestat] mean and std.dev: (232.09, 60.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[M::mem_pestat] skip orientation RR
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 284561, 1, 6)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (207, 306, 424)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 858)
[M::mem_pestat] mean and std.dev: (324.82, 151.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1075)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 682700 reads in 127.805 CPU sec, 4.108 real sec
sorting block 34, #reads = 1070791 mem = 536883244 peak = 988749824
[M::mem_process_seqs] Processed 682208 reads in 82.325 CPU sec, 2.663 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 168283, 1, 3)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (207, 308, 429)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 873)
[M::mem_pestat] mean and std.dev: (328.04, 155.30)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1095)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 403976 reads in 44.555 CPU sec, 1.483 real sec
sorting block 35, #reads = 1070473 mem = 536878142 peak = 1054969856
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 38681628
overall: 69863079936 mem 6417.860 user 217.475 sys 225.424 real
[main] Version: 0.7.17-r1188
[main] CMD: /opt/conda/share/sentieon-202308.03-3/libexec/bwa mem -K 100000000 -Y -R @RG\tID:B23KGCJLT4.NA12878_c_0002_gDNA_0004_B23KGCJLT4_1.L002\tPU:L002\tSM:NA12878_c_0002_gDNA_0004_B23KGCJLT4_1\tLB:NA12878_c_0002_gDNA_0004_B23KGCJLT4_1\tDS:s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta\tPL:ILLUMINA -t 31 ./BWAIndex/Homo_sapiens_assembly38.fasta.64 NA12878_c_0002_gDNA_0004_B23KGCJLT4_1_R1.fastq.gz NA12878_c_0002_gDNA_0004_B23KGCJLT4_1_R2.fastq.gz
[main] Real time: 225.471 sec; CPU: 6635.338 sec
sorting block 36, #reads = 320183 mem = 160564729 peak = 1054969856
uniq header count 1
merging 37 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: util-sort
license: sentieon:util=1
output file size: 1948495253
output reads: 38869527
bam_mem_sort: 37 calls 22.042 user 0.345 sys 22.415 real
bam_write: 37 calls 12.335 user 0.604 sys 12.979 real
execute: 1 calls 11.378 user 0.484 sys 239.065 real
merge_files: 1 calls 11.335 user 0.460 sys 13.171 real
parse_chunk: 581 calls 34.170 user 7.607 sys 42.215 real
read_chunk: 1570 calls 13.888 user 10.873 sys 161.985 real
sort_block: 1 calls 10.947 user 10.599 sys 156.953 real
write_chunk: 987 calls 11.059 user 0.312 sys 12.695 real
overall: 2384539648 mem 532.803 user 25.925 sys 239.089 real
ls: cannot access '*.cram': No such file or directory