cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o 659_cuO-T1-TDNA-1_A23MHWWLT4_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 1505.794 CPU sec, 54.165 real sec
[M::process] read 723980 sequences (100000247 bp) in 1.039 CPU sec, 1.045 real sec...
[M::process] read 720270 sequences (100000031 bp) in 1.490 CPU sec, 1.484 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299526, 5, 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: (137, 199, 283)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 575)
[M::mem_pestat] mean and std.dev: (217.44, 105.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 721)
[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 719146 sequences (100000123 bp) in 1.320 CPU sec, 1.323 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 298511, 10, 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: (140, 203, 289)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 587)
[M::mem_pestat] mean and std.dev: (222.14, 107.35)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 736)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (126, 595, 764)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2040)
[M::mem_pestat] mean and std.dev: (453.70, 378.81)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2678)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::process] read 719142 sequences (100000199 bp) in 1.399 CPU sec, 1.398 real sec...
[M::mem_process_seqs] Processed 723980 reads in 136.920 CPU sec, 4.289 real sec
[M::mem_process_seqs] Processed 720270 reads in 90.180 CPU sec, 2.848 real sec
sorting block 0, #reads = 1112281 mem = 536884988 peak = 601051136
[M::process] read 723124 sequences (100000088 bp) in 1.859 CPU sec, 1.910 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 298219, 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: (141, 205, 291)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 591)
[M::mem_pestat] mean and std.dev: (223.97, 107.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 741)
[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 721084 sequences (100000192 bp) in 1.510 CPU sec, 1.510 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 297640, 3, 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: (141, 204, 289)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 585)
[M::mem_pestat] mean and std.dev: (222.82, 106.91)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 733)
[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 719146 reads in 141.627 CPU sec, 4.481 real sec
[M::mem_process_seqs] Processed 719142 reads in 159.503 CPU sec, 5.065 real sec
sorting block 1, #reads = 1108543 mem = 536878514 peak = 731598848
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299634, 4, 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: (137, 200, 284)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 578)
[M::mem_pestat] mean and std.dev: (218.65, 105.48)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 725)
[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 719614 sequences (100000227 bp) in 2.152 CPU sec, 2.187 real sec...
[M::process] read 719554 sequences (100000271 bp) in 1.420 CPU sec, 1.418 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 298685, 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: (139, 204, 291)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 595)
[M::mem_pestat] mean and std.dev: (223.02, 108.43)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 747)
[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 723124 reads in 142.009 CPU sec, 4.491 real sec
sorting block 2, #reads = 1111205 mem = 536879051 peak = 832159744
[M::mem_process_seqs] Processed 721084 reads in 94.334 CPU sec, 3.001 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 298598, 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: (141, 205, 290)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 588)
[M::mem_pestat] mean and std.dev: (223.28, 107.62)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 737)
[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 722644 sequences (100000042 bp) in 2.585 CPU sec, 2.624 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 298483, 2, 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: (140, 204, 288)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 584)
[M::mem_pestat] mean and std.dev: (222.03, 106.88)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 732)
[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 719614 reads in 146.189 CPU sec, 4.601 real sec
[M::process] read 719592 sequences (100000086 bp) in 2.069 CPU sec, 2.063 real sec...
sorting block 3, #reads = 1112126 mem = 536887350 peak = 832159744
[M::mem_process_seqs] Processed 719554 reads in 97.827 CPU sec, 3.078 real sec
sorting block 4, #reads = 1110354 mem = 536877221 peak = 912867328
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 298800, 7, 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: (138, 201, 285)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 579)
[M::mem_pestat] mean and std.dev: (219.25, 105.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 726)
[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 718550 sequences (100000064 bp) in 2.528 CPU sec, 2.720 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 298271, 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: (140, 206, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 599)
[M::mem_pestat] mean and std.dev: (224.81, 109.25)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 752)
[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 719344 sequences (100000129 bp) in 1.520 CPU sec, 1.511 real sec...
[M::mem_process_seqs] Processed 722644 reads in 145.395 CPU sec, 4.600 real sec
[M::mem_process_seqs] Processed 719592 reads in 94.870 CPU sec, 3.005 real sec
sorting block 5, #reads = 1110571 mem = 536879343 peak = 912867328
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 298143, 2, 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: (141, 205, 290)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 588)
[M::mem_pestat] mean and std.dev: (223.26, 106.57)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 737)
[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 722678 sequences (100000270 bp) in 2.697 CPU sec, 2.745 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 297933, 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: (141, 204, 289)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 585)
[M::mem_pestat] mean and std.dev: (222.51, 106.70)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 733)
[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 718550 reads in 144.097 CPU sec, 4.541 real sec
[M::mem_process_seqs] Processed 719344 reads in 96.697 CPU sec, 3.035 real sec
[M::process] read 720148 sequences (100000140 bp) in 2.238 CPU sec, 2.243 real sec...
sorting block 6, #reads = 1109729 mem = 536878708 peak = 912867328
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 299176, 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: (138, 201, 285)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 579)
[M::mem_pestat] mean and std.dev: (219.43, 106.09)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 726)
[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 718848 sequences (100000180 bp) in 2.761 CPU sec, 2.961 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 298437, 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: (140, 205, 291)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 593)
[M::mem_pestat] mean and std.dev: (223.72, 108.76)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 744)
[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 722678 reads in 145.967 CPU sec, 4.640 real sec
sorting block 7, #reads = 1109224 mem = 536878408 peak = 912867328
[M::mem_process_seqs] Processed 720148 reads in 96.563 CPU sec, 3.051 real sec
[M::process] read 719112 sequences (100000099 bp) in 1.791 CPU sec, 1.810 real sec...
sorting block 8, #reads = 1111542 mem = 536879049 peak = 912867328
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 297983, 7, 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: (141, 205, 289)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 585)
[M::mem_pestat] mean and std.dev: (222.75, 106.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 733)
[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 728746 sequences (100000060 bp) in 2.474 CPU sec, 2.545 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 297680, 5, 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: (141, 205, 288)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 582)
[M::mem_pestat] mean and std.dev: (222.24, 106.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 729)
[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: (280, 470, 807)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1861)
[M::mem_pestat] mean and std.dev: (429.64, 242.16)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2388)
[M::mem_pestat] skip orientation RR
[M::process] read 724580 sequences (100000291 bp) in 1.630 CPU sec, 1.633 real sec...
[M::mem_process_seqs] Processed 718848 reads in 145.245 CPU sec, 4.594 real sec
[M::mem_process_seqs] Processed 719112 reads in 96.582 CPU sec, 3.050 real sec
sorting block 9, #reads = 1108583 mem = 536880209 peak = 912867328
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 301456, 3, 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: (132, 192, 272)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 552)
[M::mem_pestat] mean and std.dev: (210.13, 101.88)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 692)
[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 722384 sequences (100000234 bp) in 2.817 CPU sec, 2.874 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 300741, 4, 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: (136, 197, 281)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 571)
[M::mem_pestat] mean and std.dev: (217.18, 106.54)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 716)
[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 728746 reads in 151.372 CPU sec, 4.770 real sec
[M::process] read 723730 sequences (100000009 bp) in 1.987 CPU sec, 1.993 real sec...
[M::mem_process_seqs] Processed 724580 reads in 100.701 CPU sec, 3.169 real sec
sorting block 10, #reads = 1110842 mem = 536879394 peak = 912867328
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299490, 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: (138, 200, 285)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 579)
[M::mem_pestat] mean and std.dev: (219.63, 107.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 726)
[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 730012 sequences (100000178 bp) in 2.616 CPU sec, 2.673 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 299451, 1, 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: (137, 198, 281)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 569)
[M::mem_pestat] mean and std.dev: (216.77, 105.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 713)
[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 722384 reads in 156.993 CPU sec, 4.948 real sec
[M::process] read 726168 sequences (100000097 bp) in 2.328 CPU sec, 2.325 real sec...
sorting block 11, #reads = 1110827 mem = 536879965 peak = 912867328
[M::mem_process_seqs] Processed 723730 reads in 106.136 CPU sec, 3.346 real sec
sorting block 12, #reads = 1108076 mem = 536878402 peak = 912867328
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 302030, 4, 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: (132, 190, 270)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 546)
[M::mem_pestat] mean and std.dev: (208.84, 100.98)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 684)
[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 723056 sequences (100000101 bp) in 2.453 CPU sec, 2.529 real sec...
[M::process] read 726394 sequences (100000096 bp) in 1.690 CPU sec, 1.699 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 300979, 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: (135, 195, 278)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 564)
[M::mem_pestat] mean and std.dev: (214.28, 104.08)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 707)
[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 730012 reads in 164.428 CPU sec, 5.213 real sec
[M::mem_process_seqs] Processed 726168 reads in 107.404 CPU sec, 3.413 real sec
sorting block 13, #reads = 1108845 mem = 536878753 peak = 912867328
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 299470, 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: (137, 199, 282)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 572)
[M::mem_pestat] mean and std.dev: (217.98, 106.39)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 717)
[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 725098 sequences (100000090 bp) in 2.934 CPU sec, 2.984 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 300750, 4, 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: (134, 195, 276)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 560)
[M::mem_pestat] mean and std.dev: (213.26, 103.40)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 702)
[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 723056 reads in 158.770 CPU sec, 5.016 real sec
[M::mem_process_seqs] Processed 726394 reads in 109.142 CPU sec, 3.430 real sec
[M::process] read 722726 sequences (100000173 bp) in 2.390 CPU sec, 2.404 real sec...
sorting block 14, #reads = 1109498 mem = 536883864 peak = 912867328
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 300649, 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: (135, 197, 279)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 567)
[M::mem_pestat] mean and std.dev: (215.46, 104.69)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 711)
[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 721466 sequences (100000203 bp) in 2.765 CPU sec, 2.809 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299356, 3, 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: (137, 201, 286)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 584)
[M::mem_pestat] mean and std.dev: (220.24, 107.95)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 733)
[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 725098 reads in 152.987 CPU sec, 4.945 real sec
[M::mem_process_seqs] Processed 722726 reads in 102.529 CPU sec, 3.219 real sec
sorting block 15, #reads = 1110048 mem = 536877553 peak = 912867328
[M::process] read 730588 sequences (100000088 bp) in 2.349 CPU sec, 2.377 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 298619, 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: (138, 200, 284)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 576)
[M::mem_pestat] mean and std.dev: (219.63, 106.66)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 722)
[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: (135, 507, 1429)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4017)
[M::mem_pestat] mean and std.dev: (724.30, 611.08)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 5311)
[M::mem_pestat] skip orientation RR
[M::process] read 725038 sequences (100000018 bp) in 2.903 CPU sec, 2.949 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 301862, 3, 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: (131, 189, 267)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 539)
[M::mem_pestat] mean and std.dev: (206.92, 99.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 675)
[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 721466 reads in 163.011 CPU sec, 5.148 real sec
sorting block 16, #reads = 1110454 mem = 536878158 peak = 912867328
[M::process] read 722138 sequences (100000062 bp) in 2.309 CPU sec, 2.323 real sec...
[M::mem_process_seqs] Processed 730588 reads in 113.856 CPU sec, 3.578 real sec
sorting block 17, #reads = 1106111 mem = 536882042 peak = 999411712
[M::process] read 487756 sequences (67562173 bp) in 1.818 CPU sec, 1.886 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 300834, 4, 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: (136, 197, 279)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 565)
[M::mem_pestat] mean and std.dev: (215.76, 104.77)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 708)
[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): (4, 201721, 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: (138, 200, 284)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 576)
[M::mem_pestat] mean and std.dev: (219.13, 106.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 722)
[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): (5, 299146, 4, 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: (138, 200, 283)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 573)
[M::mem_pestat] mean and std.dev: (218.43, 105.51)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 718)
[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 725038 reads in 199.507 CPU sec, 6.420 real sec
[M::mem_process_seqs] Processed 487756 reads in 140.522 CPU sec, 4.552 real sec
sorting block 18, #reads = 1109152 mem = 536878649 peak = 999411712
[M::mem_process_seqs] Processed 722138 reads in 158.277 CPU sec, 5.142 real sec
sorting block 19, #reads = 1108190 mem = 536879500 peak = 1073217536
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: 22166710
overall: 69710741504 mem 3924.677 user 160.009 sys 143.374 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:A23MHWWLT4.659_cuO-T1-TDNA-1_A23MHWWLT4_1.L007\tPU:L007\tSM:659_cuO-T1-TDNA-1_A23MHWWLT4_1\tLB:659_cuO-T1-TDNA-1_A23MHWWLT4_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_cuO-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz 659_cuO-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz
[main] Real time: 143.413 sec; CPU: 4084.689 sec
sorting block 20, #reads = 74553 mem = 35976006 peak = 1073217536
uniq header count 1
merging 21 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: 1247061460
output reads: 22270754
bam_mem_sort: 21 calls 10.423 user 0.179 sys 10.595 real
bam_write: 21 calls 8.827 user 0.297 sys 9.163 real
execute: 1 calls 5.542 user 0.495 sys 151.315 real
merge_files: 1 calls 5.530 user 0.456 sys 7.833 real
parse_chunk: 322 calls 18.089 user 3.855 sys 22.171 real
read_chunk: 872 calls 7.126 user 6.213 sys 86.591 real
sort_block: 1 calls 5.653 user 5.977 sys 83.958 real
write_chunk: 548 calls 5.159 user 0.315 sys 7.084 real
overall: 2167111680 mem 294.481 user 16.825 sys 151.339 real
ls: cannot access '*.cram': No such file or directory