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 1843.436 CPU sec, 64.935 real sec
[M::process] read 725330 sequences (100000099 bp) in 1.232 CPU sec, 1.241 real sec...
[M::process] read 722566 sequences (100000079 bp) in 1.399 CPU sec, 1.459 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 300195, 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: (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: (215.28, 103.96)
[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 719300 sequences (100000267 bp) in 1.325 CPU sec, 1.348 real sec...
[M::process] read 719412 sequences (100000088 bp) in 1.337 CPU sec, 1.345 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299255, 5, 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: (138, 202, 289)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 591)
[M::mem_pestat] mean and std.dev: (221.50, 108.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 742)
[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 725330 reads in 148.271 CPU sec, 4.742 real sec
[M::mem_process_seqs] Processed 722566 reads in 86.277 CPU sec, 2.767 real sec
sorting block 0, #reads = 1111558 mem = 536879350 peak = 603586560
[M::process] read 725082 sequences (100000203 bp) in 1.716 CPU sec, 1.750 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 298170, 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: (141, 206, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 597)
[M::mem_pestat] mean and std.dev: (224.95, 108.77)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 749)
[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 722682 sequences (100000003 bp) in 1.410 CPU sec, 1.412 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 298023, 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: (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: (222.73, 106.78)
[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_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 300353, 7, 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: (136, 197, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 568)
[M::mem_pestat] mean and std.dev: (215.52, 104.28)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 712)
[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 719300 reads in 185.928 CPU sec, 5.941 real sec
[M::mem_process_seqs] Processed 719412 reads in 143.094 CPU sec, 4.605 real sec
sorting block 1, #reads = 1109102 mem = 536881768 peak = 734777344
[M::mem_process_seqs] Processed 725082 reads in 158.140 CPU sec, 5.096 real sec
sorting block 2, #reads = 1111138 mem = 536878906 peak = 909242368
[M::process] read 720096 sequences (100000241 bp) in 1.907 CPU sec, 1.964 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 299786, 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: (138, 202, 287)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 585)
[M::mem_pestat] mean and std.dev: (220.74, 107.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 734)
[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 720222 sequences (100000277 bp) in 1.647 CPU sec, 1.662 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 298531, 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: (140, 204, 290)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 590)
[M::mem_pestat] mean and std.dev: (223.01, 107.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 740)
[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 722682 reads in 130.426 CPU sec, 4.124 real sec
[M::mem_process_seqs] Processed 720096 reads in 87.802 CPU sec, 2.758 real sec
[M::process] read 723872 sequences (100000133 bp) in 1.588 CPU sec, 1.612 real sec...
sorting block 3, #reads = 1112342 mem = 536877735 peak = 909242368
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 298146, 2, 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, 203, 287)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 581)
[M::mem_pestat] mean and std.dev: (221.24, 106.02)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 728)
[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 721742 sequences (100000292 bp) in 1.851 CPU sec, 1.886 real sec...
[M::process] read 719390 sequences (100000048 bp) in 1.455 CPU sec, 1.456 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 299929, 6, 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: (217.85, 105.38)
[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::mem_process_seqs] Processed 720222 reads in 135.352 CPU sec, 4.294 real sec
sorting block 4, #reads = 1109477 mem = 536880889 peak = 909242368
[M::mem_process_seqs] Processed 723872 reads in 87.024 CPU sec, 2.839 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 299024, 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: (138, 202, 288)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 588)
[M::mem_pestat] mean and std.dev: (221.58, 108.06)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 738)
[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 722050 sequences (100000111 bp) in 1.964 CPU sec, 2.001 real sec...
[M::process] read 722848 sequences (100000108 bp) in 1.460 CPU sec, 1.464 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 298087, 5, 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, 204, 290)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 588)
[M::mem_pestat] mean and std.dev: (223.22, 107.48)
[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::mem_process_seqs] Processed 721742 reads in 133.396 CPU sec, 4.299 real sec
sorting block 5, #reads = 1112195 mem = 536880799 peak = 909242368
[M::mem_process_seqs] Processed 719390 reads in 86.315 CPU sec, 2.804 real sec
sorting block 6, #reads = 1111138 mem = 536881988 peak = 920883200
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 298974, 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: (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: (219.59, 105.79)
[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 721008 sequences (100000279 bp) in 1.875 CPU sec, 1.921 real sec...
[M::process] read 718142 sequences (100000151 bp) in 1.550 CPU sec, 1.547 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299331, 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: (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: (219.73, 107.05)
[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::mem_process_seqs] Processed 722050 reads in 136.913 CPU sec, 4.404 real sec
[M::mem_process_seqs] Processed 722848 reads in 86.979 CPU sec, 2.757 real sec
sorting block 7, #reads = 1110378 mem = 536885966 peak = 920883200
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 298953, 10, 6)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (264, 264, 327)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (138, 453)
[M::mem_pestat] mean and std.dev: (253.44, 53.32)
[M::mem_pestat] low and high boundaries for proper pairs: (40, 516)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (139, 203, 290)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 592)
[M::mem_pestat] mean and std.dev: (222.93, 109.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 743)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (138, 1825, 2677)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7755)
[M::mem_pestat] mean and std.dev: (1834.70, 1880.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 10294)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::process] read 723106 sequences (100000089 bp) in 2.046 CPU sec, 2.105 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 298151, 6, 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: (142, 206, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 592)
[M::mem_pestat] mean and std.dev: (224.62, 107.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 742)
[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 727902 sequences (100000012 bp) in 1.690 CPU sec, 1.683 real sec...
[M::mem_process_seqs] Processed 721008 reads in 133.617 CPU sec, 4.223 real sec
[M::mem_process_seqs] Processed 718142 reads in 91.621 CPU sec, 2.898 real sec
sorting block 8, #reads = 1111857 mem = 536877790 peak = 920883200
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 299719, 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: (138, 199, 282)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 570)
[M::mem_pestat] mean and std.dev: (217.54, 104.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 714)
[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 725612 sequences (100000158 bp) in 2.047 CPU sec, 2.089 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 301103, 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: (133, 193, 275)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 559)
[M::mem_pestat] mean and std.dev: (212.07, 103.43)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 701)
[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 722406 sequences (100000196 bp) in 1.740 CPU sec, 1.736 real sec...
[M::mem_process_seqs] Processed 723106 reads in 141.902 CPU sec, 4.491 real sec
sorting block 9, #reads = 1107855 mem = 536878560 peak = 920883200
[M::mem_process_seqs] Processed 727902 reads in 93.493 CPU sec, 2.952 real sec
sorting block 10, #reads = 1112290 mem = 536879137 peak = 920883200
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 300730, 6, 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: (135, 196, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 570)
[M::mem_pestat] mean and std.dev: (215.66, 105.62)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 715)
[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 730350 sequences (100000122 bp) in 2.134 CPU sec, 2.183 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299488, 7, 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, 286)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 582)
[M::mem_pestat] mean and std.dev: (220.42, 107.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 730)
[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 729482 sequences (100000215 bp) in 1.708 CPU sec, 1.717 real sec...
[M::mem_process_seqs] Processed 725612 reads in 143.154 CPU sec, 4.537 real sec
[M::mem_process_seqs] Processed 722406 reads in 95.413 CPU sec, 3.026 real sec
sorting block 11, #reads = 1111985 mem = 536880465 peak = 920883200
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 302021, 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: (131, 190, 267)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 539)
[M::mem_pestat] mean and std.dev: (207.13, 99.31)
[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::process] read 725764 sequences (100000174 bp) in 2.368 CPU sec, 2.415 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 302184, 3, 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: (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: (209.10, 101.15)
[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 723216 sequences (100000145 bp) in 2.119 CPU sec, 2.119 real sec...
[M::mem_process_seqs] Processed 730350 reads in 158.377 CPU sec, 5.002 real sec
[M::mem_process_seqs] Processed 729482 reads in 103.462 CPU sec, 3.266 real sec
sorting block 12, #reads = 1108616 mem = 536882193 peak = 920883200
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 300640, 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: (135, 195, 277)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 561)
[M::mem_pestat] mean and std.dev: (214.12, 103.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 703)
[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 727060 sequences (100000245 bp) in 2.172 CPU sec, 2.229 real sec...
[M::process] read 724180 sequences (100000205 bp) in 1.649 CPU sec, 1.651 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 299260, 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: (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: (216.79, 104.87)
[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 725764 reads in 152.022 CPU sec, 4.914 real sec
sorting block 13, #reads = 1110842 mem = 536881926 peak = 920883200
[M::mem_process_seqs] Processed 723216 reads in 100.124 CPU sec, 3.187 real sec
sorting block 14, #reads = 1108244 mem = 536880240 peak = 920883200
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 301140, 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: (134, 193, 273)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 551)
[M::mem_pestat] mean and std.dev: (211.39, 101.77)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 690)
[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 722262 sequences (100000082 bp) in 2.615 CPU sec, 2.663 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 300558, 5, 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, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 568)
[M::mem_pestat] mean and std.dev: (216.20, 104.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 712)
[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 727060 reads in 143.644 CPU sec, 4.552 real sec
[M::mem_process_seqs] Processed 724180 reads in 95.575 CPU sec, 3.007 real sec
[M::process] read 726994 sequences (100000094 bp) in 2.409 CPU sec, 2.428 real sec...
sorting block 15, #reads = 1112851 mem = 536878098 peak = 920883200
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 299330, 5, 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: (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: (218.75, 106.06)
[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::process] read 728552 sequences (100000050 bp) in 2.528 CPU sec, 2.584 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 300420, 0, 0)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (159, 283, 375)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 807)
[M::mem_pestat] mean and std.dev: (265.18, 111.08)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1023)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (134, 193, 273)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 551)
[M::mem_pestat] mean and std.dev: (211.34, 102.02)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 690)
[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 722262 reads in 153.841 CPU sec, 4.880 real sec
[M::process] read 722394 sequences (100000097 bp) in 1.717 CPU sec, 1.722 real sec...
[M::mem_process_seqs] Processed 726994 reads in 108.386 CPU sec, 3.548 real sec
sorting block 16, #reads = 1110421 mem = 536879147 peak = 920883200
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 301564, 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: (133, 192, 273)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 553)
[M::mem_pestat] mean and std.dev: (211.06, 102.43)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 693)
[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 720554 sequences (100000062 bp) in 2.249 CPU sec, 2.328 real sec...
[M::process] read 153886 sequences (21327466 bp) in 0.530 CPU sec, 0.521 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299570, 6, 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, 199, 283)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 573)
[M::mem_pestat] mean and std.dev: (218.40, 105.77)
[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 728552 reads in 150.268 CPU sec, 4.915 real sec
sorting block 17, #reads = 1105919 mem = 536878731 peak = 920883200
[M::mem_process_seqs] Processed 722394 reads in 98.880 CPU sec, 3.184 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 298861, 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, 202, 286)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 578)
[M::mem_pestat] mean and std.dev: (220.75, 106.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 724)
[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): (3, 63548, 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: (138, 201, 286)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 582)
[M::mem_pestat] mean and std.dev: (220.45, 107.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 730)
[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 720554 reads in 93.413 CPU sec, 3.033 real sec
sorting block 18, #reads = 1108529 mem = 536879413 peak = 1077850112
[M::mem_process_seqs] Processed 153886 reads in 33.485 CPU sec, 1.089 real sec
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: 21857462
overall: 69859508224 mem 4031.809 user 190.548 sys 147.753 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.L005\tPU:L005\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: 147.811 sec; CPU: 4222.379 sec
sorting block 19, #reads = 862738 mem = 418100165 peak = 1077850112
uniq header count 1
merging 20 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: 1251550933
output reads: 21959475
bam_mem_sort: 20 calls 8.769 user 0.239 sys 9.048 real
bam_write: 20 calls 9.007 user 0.367 sys 9.420 real
execute: 1 calls 5.302 user 0.442 sys 156.491 real
merge_files: 1 calls 5.297 user 0.395 sys 7.818 real
parse_chunk: 317 calls 16.529 user 3.408 sys 20.285 real
read_chunk: 859 calls 6.876 user 5.675 sys 79.633 real
sort_block: 1 calls 5.916 user 5.440 sys 77.727 real
write_chunk: 540 calls 5.018 user 0.227 sys 7.105 real
overall: 2194714624 mem 290.173 user 14.693 sys 156.513 real
ls: cannot access '*.cram': No such file or directory