cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o 659_wQ-N1-BDNA-1_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.
No more license available for sentieon:klib
version: sentieon-genomics-202308.03
No more license available for sentieon:klib
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
No more license available for sentieon:klib
No more license available for sentieon:klib
[M::main_mem] bwa index loaded in 1611.870 CPU sec, 234.846 real sec
[M::process] read 688340 sequences (100000188 bp) in 0.911 CPU sec, 0.917 real sec...
[M::process] read 686944 sequences (100000098 bp) in 1.178 CPU sec, 1.237 real sec...
[M::process] read 686274 sequences (100000271 bp) in 1.168 CPU sec, 1.171 real sec...
[M::process] read 685336 sequences (100000270 bp) in 1.130 CPU sec, 1.128 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284254, 1, 1)
[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: (192, 290, 409)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 843)
[M::mem_pestat] mean and std.dev: (310.99, 150.51)
[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::mem_process_seqs] Processed 686944 reads in 70.617 CPU sec, 2.265 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 284623, 1, 0)
[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: (189, 284, 401)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 825)
[M::mem_pestat] mean and std.dev: (304.92, 147.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1037)
[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 684908 sequences (100000177 bp) in 1.129 CPU sec, 1.135 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 284420, 0, 2)
[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: (195, 296, 419)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 867)
[M::mem_pestat] mean and std.dev: (317.54, 155.08)
[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 688340 reads in 222.297 CPU sec, 7.117 real sec
[M::mem_process_seqs] Processed 686274 reads in 149.831 CPU sec, 4.804 real sec
sorting block 0, #reads = 1090564 mem = 536887878 peak = 608104448
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 284054, 0, 0)
[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, 300, 424)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 878)
[M::mem_pestat] mean and std.dev: (321.71, 156.74)
[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] skip orientation RR as there are not enough pairs
[M::process] read 686076 sequences (100000128 bp) in 1.698 CPU sec, 1.802 real sec...
[M::process] read 687042 sequences (100000116 bp) in 1.280 CPU sec, 1.281 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 283891, 1, 2)
[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, 300, 424)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 874)
[M::mem_pestat] mean and std.dev: (322.16, 156.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1099)
[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 685336 reads in 129.776 CPU sec, 4.134 real sec
sorting block 1, #reads = 1090137 mem = 536876744 peak = 855953408
[M::mem_process_seqs] Processed 684908 reads in 81.508 CPU sec, 2.611 real sec
sorting block 2, #reads = 1087888 mem = 536880080 peak = 891817984
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 284306, 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: (194, 292, 415)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 857)
[M::mem_pestat] mean and std.dev: (315.21, 153.70)
[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 686146 sequences (100000092 bp) in 2.044 CPU sec, 2.211 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 284372, 1, 0)
[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: (193, 291, 411)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 847)
[M::mem_pestat] mean and std.dev: (312.25, 151.21)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1065)
[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 685846 sequences (100000081 bp) in 1.422 CPU sec, 1.427 real sec...
[M::mem_process_seqs] Processed 686076 reads in 133.264 CPU sec, 4.239 real sec
[M::mem_process_seqs] Processed 687042 reads in 82.526 CPU sec, 2.620 real sec
sorting block 3, #reads = 1090661 mem = 536878773 peak = 891817984
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 284037, 2, 2)
[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: (195, 295, 419)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 867)
[M::mem_pestat] mean and std.dev: (316.84, 153.71)
[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::process] read 685132 sequences (100000007 bp) in 2.155 CPU sec, 2.267 real sec...
[M::process] read 685534 sequences (100000282 bp) in 1.300 CPU sec, 1.300 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 283350, 0, 1)
[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: (196, 297, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 871)
[M::mem_pestat] mean and std.dev: (319.46, 155.70)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1096)
[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 686146 reads in 134.416 CPU sec, 4.285 real sec
[M::mem_process_seqs] Processed 685846 reads in 85.380 CPU sec, 2.716 real sec
sorting block 4, #reads = 1089203 mem = 536879413 peak = 891817984
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 283793, 0, 0)
[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, 299, 423)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 875)
[M::mem_pestat] mean and std.dev: (320.71, 155.61)
[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 687266 sequences (100000122 bp) in 1.864 CPU sec, 1.989 real sec...
[M::process] read 686680 sequences (100000263 bp) in 1.310 CPU sec, 1.302 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 283905, 2, 1)
[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: (195, 293, 418)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 864)
[M::mem_pestat] mean and std.dev: (317.53, 155.93)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1087)
[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 685132 reads in 134.843 CPU sec, 4.314 real sec
[M::mem_process_seqs] Processed 685534 reads in 84.666 CPU sec, 2.699 real sec
sorting block 5, #reads = 1088283 mem = 536878322 peak = 891817984
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 284485, 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: (191, 289, 409)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 845)
[M::mem_pestat] mean and std.dev: (310.91, 151.64)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1063)
[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 685450 sequences (100000192 bp) in 2.021 CPU sec, 2.155 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284462, 0, 1)
[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: (195, 295, 416)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 858)
[M::mem_pestat] mean and std.dev: (315.69, 152.90)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1079)
[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 684814 sequences (100000050 bp) in 1.670 CPU sec, 1.674 real sec...
[M::mem_process_seqs] Processed 687266 reads in 136.349 CPU sec, 4.346 real sec
sorting block 6, #reads = 1088539 mem = 536879474 peak = 891817984
[M::mem_process_seqs] Processed 686680 reads in 84.256 CPU sec, 2.678 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 283758, 0, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
sorting block 7, #reads = 1090426 mem = 536888370 peak = 937537536
[M::mem_pestat] (25, 50, 75) percentile: (197, 299, 423)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 875)
[M::mem_pestat] mean and std.dev: (320.60, 155.32)
[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 685134 sequences (100000157 bp) in 2.003 CPU sec, 2.147 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 283735, 1, 1)
[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, 301, 425)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 877)
[M::mem_pestat] mean and std.dev: (322.53, 156.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1103)
[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 686082 sequences (100000046 bp) in 1.360 CPU sec, 1.368 real sec...
[M::mem_process_seqs] Processed 685450 reads in 135.457 CPU sec, 4.332 real sec
[M::mem_process_seqs] Processed 684814 reads in 85.165 CPU sec, 2.706 real sec
sorting block 8, #reads = 1089204 mem = 536879178 peak = 937537536
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 283649, 0, 0)
[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: (196, 295, 419)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 865)
[M::mem_pestat] mean and std.dev: (318.79, 156.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1088)
[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 686916 sequences (100000157 bp) in 2.476 CPU sec, 2.631 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 283996, 1, 0)
[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: (194, 293, 418)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 866)
[M::mem_pestat] mean and std.dev: (317.40, 156.97)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1090)
[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 685760 sequences (100000295 bp) in 1.380 CPU sec, 1.372 real sec...
[M::mem_process_seqs] Processed 685134 reads in 136.413 CPU sec, 4.344 real sec
[M::mem_process_seqs] Processed 686082 reads in 86.262 CPU sec, 2.737 real sec
sorting block 9, #reads = 1088249 mem = 536879895 peak = 937537536
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 284196, 3, 0)
[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: (192, 291, 412)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 852)
[M::mem_pestat] mean and std.dev: (313.00, 152.78)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1072)
[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 684766 sequences (100000264 bp) in 1.942 CPU sec, 2.079 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 283523, 0, 2)
[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, 297, 420)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 866)
[M::mem_pestat] mean and std.dev: (319.00, 155.12)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1089)
[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 685286 sequences (100000057 bp) in 1.440 CPU sec, 1.437 real sec...
[M::mem_process_seqs] Processed 686916 reads in 136.618 CPU sec, 4.368 real sec
sorting block 10, #reads = 1089404 mem = 536882263 peak = 937537536
[M::mem_process_seqs] Processed 685760 reads in 86.172 CPU sec, 2.742 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 283591, 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: (199, 300, 424)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 874)
[M::mem_pestat] mean and std.dev: (322.20, 156.11)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1099)
[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 11, #reads = 1088873 mem = 536880819 peak = 937537536
[M::process] read 685648 sequences (100000098 bp) in 2.611 CPU sec, 2.739 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 283374, 2, 1)
[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: (196, 295, 417)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 859)
[M::mem_pestat] mean and std.dev: (317.35, 154.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1080)
[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 684766 reads in 138.311 CPU sec, 4.413 real sec
[M::process] read 688938 sequences (100000135 bp) in 1.575 CPU sec, 1.602 real sec...
[M::mem_process_seqs] Processed 685286 reads in 87.534 CPU sec, 2.767 real sec
sorting block 12, #reads = 1088069 mem = 536882142 peak = 937537536
[M::process] read 688616 sequences (100000119 bp) in 2.007 CPU sec, 2.166 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284923, 1, 1)
[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: (186, 280, 403)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 837)
[M::mem_pestat] mean and std.dev: (305.42, 152.11)
[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::process] read 688074 sequences (100000024 bp) in 1.404 CPU sec, 1.403 real sec...
[M::mem_process_seqs] Processed 688938 reads in 77.055 CPU sec, 2.434 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 283970, 0, 1)
[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: (195, 293, 417)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 861)
[M::mem_pestat] mean and std.dev: (317.32, 156.00)
[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_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 285156, 0, 2)
[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: (187, 284, 406)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 844)
[M::mem_pestat] mean and std.dev: (307.15, 150.73)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1063)
[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 685648 reads in 212.116 CPU sec, 6.768 real sec
sorting block 13, #reads = 1088242 mem = 536880095 peak = 937537536
[M::process] read 687054 sequences (100000001 bp) in 2.081 CPU sec, 2.109 real sec...
[M::mem_process_seqs] Processed 688616 reads in 99.612 CPU sec, 3.162 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 285277, 0, 1)
[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: (189, 288, 408)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 846)
[M::mem_pestat] mean and std.dev: (309.43, 151.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1065)
[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 14, #reads = 1088938 mem = 536879405 peak = 957153280
[M::process] read 686266 sequences (100000262 bp) in 2.615 CPU sec, 2.808 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284620, 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: (192, 289, 409)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 843)
[M::mem_pestat] mean and std.dev: (310.96, 150.56)
[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::mem_process_seqs] Processed 688074 reads in 139.768 CPU sec, 4.459 real sec
[M::mem_process_seqs] Processed 687054 reads in 89.158 CPU sec, 2.814 real sec
[M::process] read 686412 sequences (100000048 bp) in 1.563 CPU sec, 1.612 real sec...
sorting block 15, #reads = 1088338 mem = 536877585 peak = 957153280
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284309, 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: (193, 291, 407)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 835)
[M::mem_pestat] mean and std.dev: (310.49, 148.40)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1049)
[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 689498 sequences (100000147 bp) in 2.075 CPU sec, 2.199 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 284651, 0, 2)
[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: (192, 289, 405)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 831)
[M::mem_pestat] mean and std.dev: (309.44, 148.81)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1044)
[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 686266 reads in 138.385 CPU sec, 4.404 real sec
[M::mem_process_seqs] Processed 686412 reads in 93.084 CPU sec, 2.929 real sec
[M::process] read 687964 sequences (100000077 bp) in 1.881 CPU sec, 1.910 real sec...
sorting block 16, #reads = 1087660 mem = 536880303 peak = 957153280
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 285437, 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: (185, 278, 396)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 818)
[M::mem_pestat] mean and std.dev: (300.38, 146.29)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1029)
[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 687648 sequences (100000045 bp) in 2.820 CPU sec, 2.961 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 284913, 0, 2)
[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: (189, 286, 404)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 834)
[M::mem_pestat] mean and std.dev: (306.90, 148.47)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1049)
[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 689498 reads in 152.690 CPU sec, 4.846 real sec
[M::mem_process_seqs] Processed 687964 reads in 98.195 CPU sec, 3.089 real sec
sorting block 17, #reads = 1087936 mem = 536878397 peak = 957153280
[M::process] read 686526 sequences (100000039 bp) in 2.229 CPU sec, 2.304 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 285384, 1, 0)
[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: (190, 286, 405)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 835)
[M::mem_pestat] mean and std.dev: (307.85, 149.29)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1050)
[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 = 1088693 mem = 536878109 peak = 957153280
[M::process] read 686436 sequences (100000222 bp) in 2.611 CPU sec, 2.722 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 285211, 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: (193, 290, 410)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 844)
[M::mem_pestat] mean and std.dev: (311.72, 150.68)
[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 687648 reads in 159.598 CPU sec, 5.073 real sec
[M::mem_process_seqs] Processed 686526 reads in 105.581 CPU sec, 3.322 real sec
[M::process] read 688436 sequences (100000225 bp) in 2.261 CPU sec, 2.314 real sec...
sorting block 19, #reads = 1086085 mem = 536885706 peak = 957153280
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 284733, 0, 1)
[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: (194, 293, 413)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 851)
[M::mem_pestat] mean and std.dev: (314.28, 152.59)
[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] skip orientation RR as there are not enough pairs
[M::process] read 687944 sequences (100000017 bp) in 2.481 CPU sec, 2.647 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 285454, 2, 0)
[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: (188, 283, 403)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 833)
[M::mem_pestat] mean and std.dev: (305.55, 149.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1048)
[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 687002 sequences (100000102 bp) in 1.400 CPU sec, 1.402 real sec...
[M::mem_process_seqs] Processed 686436 reads in 157.457 CPU sec, 5.007 real sec
[M::mem_process_seqs] Processed 688436 reads in 104.353 CPU sec, 3.311 real sec
sorting block 20, #reads = 1086173 mem = 536878846 peak = 957153280
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 285128, 2, 0)
[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: (189, 285, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 828)
[M::mem_pestat] mean and std.dev: (305.83, 147.44)
[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 686182 sequences (100000069 bp) in 2.673 CPU sec, 2.839 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 285145, 2, 2)
[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: (192, 289, 406)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 834)
[M::mem_pestat] mean and std.dev: (309.02, 148.48)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1048)
[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 687944 reads in 147.244 CPU sec, 4.681 real sec
[M::mem_process_seqs] Processed 687002 reads in 93.267 CPU sec, 2.932 real sec
[M::process] read 685676 sequences (100000184 bp) in 1.986 CPU sec, 2.078 real sec...
sorting block 21, #reads = 1086281 mem = 536881663 peak = 957153280
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 284550, 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: (195, 293, 414)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 852)
[M::mem_pestat] mean and std.dev: (314.19, 151.57)
[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::process] read 686446 sequences (100000149 bp) in 2.821 CPU sec, 2.973 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284098, 0, 1)
[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: (195, 294, 415)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 855)
[M::mem_pestat] mean and std.dev: (315.49, 152.54)
[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 686182 reads in 154.881 CPU sec, 4.941 real sec
[M::mem_process_seqs] Processed 685676 reads in 105.028 CPU sec, 3.309 real sec
sorting block 22, #reads = 1088721 mem = 536876858 peak = 957153280
[M::process] read 688690 sequences (100000191 bp) in 2.439 CPU sec, 2.557 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 284314, 0, 2)
[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: (192, 288, 410)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 846)
[M::mem_pestat] mean and std.dev: (311.94, 152.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1064)
[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 23, #reads = 1083916 mem = 536879276 peak = 957153280
[M::process] read 687438 sequences (100000254 bp) in 2.597 CPU sec, 2.758 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 285122, 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: (187, 282, 403)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 835)
[M::mem_pestat] mean and std.dev: (305.53, 149.54)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1051)
[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 686446 reads in 156.638 CPU sec, 4.983 real sec
[M::process] read 686238 sequences (100000048 bp) in 2.390 CPU sec, 2.512 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 284997, 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: (191, 289, 413)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 857)
[M::mem_pestat] mean and std.dev: (312.21, 152.81)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1079)
[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 687438 reads in 81.885 CPU sec, 2.586 real sec
sorting block 24, #reads = 1083898 mem = 536882861 peak = 957153280
[M::process] read 685600 sequences (100000137 bp) in 2.325 CPU sec, 2.407 real sec...
[M::mem_process_seqs] Processed 688690 reads in 219.006 CPU sec, 6.911 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 284779, 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: (194, 294, 417)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 863)
[M::mem_pestat] mean and std.dev: (316.21, 153.89)
[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] skip orientation RR as there are not enough pairs
[M::process] read 685524 sequences (100000154 bp) in 2.507 CPU sec, 2.704 real sec...
[M::process] read 102494 sequences (14942763 bp) in 0.530 CPU sec, 0.532 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 283919, 5, 0)
[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: (195, 292, 412)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 846)
[M::mem_pestat] mean and std.dev: (313.79, 151.17)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1063)
[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 686238 reads in 179.553 CPU sec, 5.695 real sec
sorting block 25, #reads = 1087533 mem = 536880389 peak = 957153280
[M::mem_process_seqs] Processed 685600 reads in 103.734 CPU sec, 3.306 real sec
sorting block 26, #reads = 1083702 mem = 536878185 peak = 988774400
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 283965, 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: (195, 292, 411)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 843)
[M::mem_pestat] mean and std.dev: (313.68, 151.60)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1059)
[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): (0, 42389, 0, 0)
[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: (194, 290, 413)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 851)
[M::mem_pestat] mean and std.dev: (315.20, 155.09)
[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] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 685524 reads in 91.039 CPU sec, 2.956 real sec
[M::mem_process_seqs] Processed 102494 reads in 26.648 CPU sec, 0.861 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 30312482
overall: 69556191232 mem 4788.718 user 295.318 sys 355.168 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:B23KGCJLT4.659_wQ-N1-BDNA-1_B23KGCJLT4_1.L007\tPU:L007\tSM:659_wQ-N1-BDNA-1_B23KGCJLT4_1\tLB:659_wQ-N1-BDNA-1_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.64 659_wQ-N1-BDNA-1_B23KGCJLT4_1_R1.fastq.gz 659_wQ-N1-BDNA-1_B23KGCJLT4_1_R2.fastq.gz
[main] Real time: 355.208 sec; CPU: 5084.045 sec
sorting block 27, #reads = 1077522 mem = 532924914 peak = 988774400
uniq header count 1
merging 28 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 192
algo: util-sort
license: sentieon:util=1
output file size: 1663974713
output reads: 30453138
bam_mem_sort: 28 calls 14.231 user 0.425 sys 14.710 real
bam_write: 28 calls 5.907 user 0.399 sys 6.262 real
execute: 1 calls 8.795 user 0.518 sys 365.625 real
merge_files: 1 calls 8.764 user 0.502 sys 9.734 real
parse_chunk: 448 calls 18.890 user 4.695 sys 23.857 real
read_chunk: 1210 calls 8.789 user 9.600 sys 118.337 real
sort_block: 1 calls 7.166 user 9.064 sys 115.131 real
write_chunk: 760 calls 8.420 user 0.356 sys 9.164 real
overall: 2384105472 mem 363.924 user 19.957 sys 365.647 real
ls: cannot access '*.cram': No such file or directory