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 1490.697 CPU sec, 53.078 real sec
[M::process] read 725690 sequences (100000185 bp) in 1.104 CPU sec, 1.115 real sec...
[M::process] read 721948 sequences (100000087 bp) in 1.688 CPU sec, 1.683 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 299955, 4, 4)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (84, 135, 581)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1575)
[M::mem_pestat] mean and std.dev: (309.10, 268.85)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2072)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (135, 196, 278)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 564)
[M::mem_pestat] mean and std.dev: (214.60, 103.57)
[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_pestat] skip orientation FF
[M::process] read 717822 sequences (100000192 bp) in 1.530 CPU sec, 1.529 real sec...
[M::process] read 717472 sequences (100000229 bp) in 1.636 CPU sec, 1.673 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299165, 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: (139, 202, 287)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 583)
[M::mem_pestat] mean and std.dev: (220.91, 107.12)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 731)
[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 725690 reads in 173.192 CPU sec, 5.474 real sec
[M::mem_process_seqs] Processed 721948 reads in 110.080 CPU sec, 3.517 real sec
sorting block 0, #reads = 1113381 mem = 536878349 peak = 600469504
[M::process] read 724830 sequences (100000154 bp) in 2.142 CPU sec, 2.194 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 297980, 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: (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: (225.19, 108.39)
[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 721766 sequences (100000036 bp) in 1.601 CPU sec, 1.612 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 299314, 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: (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: (215.87, 104.52)
[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_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 297306, 3, 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: (142, 208, 294)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 598)
[M::mem_pestat] mean and std.dev: (226.05, 108.73)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 750)
[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 717822 reads in 230.381 CPU sec, 7.384 real sec
[M::mem_process_seqs] Processed 724830 reads in 176.408 CPU sec, 5.701 real sec
sorting block 1, #reads = 1109376 mem = 536878860 peak = 729444352
[M::mem_process_seqs] Processed 717472 reads in 194.806 CPU sec, 6.295 real sec
[M::process] read 718276 sequences (100000178 bp) in 2.389 CPU sec, 2.490 real sec...
sorting block 2, #reads = 1112505 mem = 536878858 peak = 754524160
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 298576, 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: (139, 202, 290)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 592)
[M::mem_pestat] mean and std.dev: (222.57, 109.29)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 743)
[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 718408 sequences (100000066 bp) in 2.006 CPU sec, 2.026 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 298186, 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: (142, 207, 294)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 598)
[M::mem_pestat] mean and std.dev: (225.97, 109.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 750)
[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 721766 reads in 155.878 CPU sec, 4.946 real sec
[M::mem_process_seqs] Processed 718276 reads in 102.784 CPU sec, 3.237 real sec
[M::process] read 725066 sequences (100000205 bp) in 2.108 CPU sec, 2.152 real sec...
sorting block 3, #reads = 1110604 mem = 536877756 peak = 754524160
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 297779, 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: (141, 206, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 594)
[M::mem_pestat] mean and std.dev: (224.54, 108.04)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 745)
[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 721374 sequences (100000129 bp) in 2.151 CPU sec, 2.207 real sec...
[M::process] read 719880 sequences (100000015 bp) in 1.497 CPU sec, 1.501 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 300448, 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: (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: (215.26, 103.73)
[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_process_seqs] Processed 718408 reads in 160.474 CPU sec, 5.095 real sec
[M::mem_process_seqs] Processed 725066 reads in 103.577 CPU sec, 3.288 real sec
sorting block 4, #reads = 1109569 mem = 536876527 peak = 754524160
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 298910, 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: (139, 202, 289)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 589)
[M::mem_pestat] mean and std.dev: (221.89, 108.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 739)
[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 718834 sequences (100000039 bp) in 2.342 CPU sec, 2.407 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 298438, 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: (140, 203, 288)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 584)
[M::mem_pestat] mean and std.dev: (222.24, 107.35)
[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::process] read 724620 sequences (100000106 bp) in 2.028 CPU sec, 2.032 real sec...
[M::mem_process_seqs] Processed 721374 reads in 155.363 CPU sec, 4.910 real sec
sorting block 5, #reads = 1111489 mem = 536877665 peak = 754524160
[M::mem_process_seqs] Processed 719880 reads in 111.484 CPU sec, 3.537 real sec
sorting block 6, #reads = 1110336 mem = 536879374 peak = 819601408
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 297600, 5, 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: (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: (223.79, 107.72)
[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] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (145, 857, 1105)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3025)
[M::mem_pestat] mean and std.dev: (712.20, 517.50)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 3985)
[M::mem_pestat] skip orientation RR
[M::process] read 721678 sequences (100000172 bp) in 2.462 CPU sec, 2.511 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 299351, 2, 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: (136, 198, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 568)
[M::mem_pestat] mean and std.dev: (216.07, 104.55)
[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::process] read 721182 sequences (100000202 bp) in 2.136 CPU sec, 2.140 real sec...
[M::mem_process_seqs] Processed 718834 reads in 162.193 CPU sec, 5.127 real sec
[M::mem_process_seqs] Processed 724620 reads in 109.707 CPU sec, 3.464 real sec
sorting block 7, #reads = 1109312 mem = 536878798 peak = 819601408
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299080, 12, 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, 202, 289)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 589)
[M::mem_pestat] mean and std.dev: (221.91, 108.62)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 739)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (781, 781, 875)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (593, 1063)
[M::mem_pestat] mean and std.dev: (791.44, 29.54)
[M::mem_pestat] low and high boundaries for proper pairs: (499, 1157)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::process] read 719584 sequences (100000244 bp) in 2.404 CPU sec, 2.473 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 298880, 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: (139, 201, 284)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 574)
[M::mem_pestat] mean and std.dev: (219.28, 105.55)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 719)
[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 730450 sequences (100000243 bp) in 1.780 CPU sec, 1.777 real sec...
[M::mem_process_seqs] Processed 721678 reads in 161.881 CPU sec, 5.205 real sec
[M::mem_process_seqs] Processed 721182 reads in 103.705 CPU sec, 3.369 real sec
sorting block 8, #reads = 1113065 mem = 536878787 peak = 819601408
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 297771, 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: (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: (221.64, 106.25)
[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 726586 sequences (100000172 bp) in 2.461 CPU sec, 2.527 real sec...
[M::process] read 722726 sequences (100000014 bp) in 1.781 CPU sec, 1.790 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 302060, 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: (131, 189, 265)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 533)
[M::mem_pestat] mean and std.dev: (206.01, 98.67)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 667)
[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 719584 reads in 170.282 CPU sec, 5.481 real sec
sorting block 9, #reads = 1111114 mem = 536879496 peak = 819601408
[M::mem_process_seqs] Processed 730450 reads in 113.619 CPU sec, 3.608 real sec
sorting block 10, #reads = 1112882 mem = 536877564 peak = 876724224
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 300862, 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: (134, 194, 274)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 554)
[M::mem_pestat] mean and std.dev: (212.18, 102.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 694)
[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 724304 sequences (100000056 bp) in 2.736 CPU sec, 2.810 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 299550, 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: (219.25, 107.26)
[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 729656 sequences (100000078 bp) in 2.249 CPU sec, 2.249 real sec...
[M::mem_process_seqs] Processed 726586 reads in 168.643 CPU sec, 5.332 real sec
[M::mem_process_seqs] Processed 722726 reads in 113.339 CPU sec, 3.690 real sec
sorting block 11, #reads = 1113777 mem = 536877284 peak = 876724224
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299816, 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: (137, 197, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 566)
[M::mem_pestat] mean and std.dev: (216.09, 104.59)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 709)
[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 725576 sequences (100000217 bp) in 2.333 CPU sec, 2.404 real sec...
[M::process] read 721750 sequences (100000281 bp) in 1.765 CPU sec, 1.766 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 301383, 2, 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: (132, 190, 268)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 540)
[M::mem_pestat] mean and std.dev: (208.05, 100.02)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 676)
[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 724304 reads in 187.588 CPU sec, 6.064 real sec
[M::mem_process_seqs] Processed 729656 reads in 126.844 CPU sec, 4.151 real sec
sorting block 12, #reads = 1107440 mem = 536879385 peak = 876724224
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 300808, 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: (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: (214.59, 104.47)
[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::process] read 728014 sequences (100000149 bp) in 2.649 CPU sec, 2.720 real sec...
[M::process] read 726012 sequences (100000282 bp) in 1.998 CPU sec, 2.000 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299362, 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, 200, 285)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 579)
[M::mem_pestat] mean and std.dev: (219.98, 107.42)
[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 725576 reads in 187.344 CPU sec, 6.049 real sec
sorting block 13, #reads = 1109680 mem = 536877334 peak = 876724224
[M::mem_process_seqs] Processed 721750 reads in 120.844 CPU sec, 3.930 real sec
sorting block 14, #reads = 1109515 mem = 536881303 peak = 876724224
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 300836, 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, 191, 271)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 547)
[M::mem_pestat] mean and std.dev: (209.54, 100.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 685)
[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 722874 sequences (100000007 bp) in 2.681 CPU sec, 2.761 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 301112, 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: (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: (214.66, 104.86)
[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::process] read 723196 sequences (100000055 bp) in 1.990 CPU sec, 1.990 real sec...
[M::mem_process_seqs] Processed 728014 reads in 184.703 CPU sec, 5.954 real sec
[M::mem_process_seqs] Processed 726012 reads in 120.895 CPU sec, 3.837 real sec
sorting block 15, #reads = 1111817 mem = 536878548 peak = 876724224
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299721, 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: (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: (219.20, 107.06)
[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 732608 sequences (100000069 bp) in 2.969 CPU sec, 3.028 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 298972, 3, 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: (137, 198, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 566)
[M::mem_pestat] mean and std.dev: (216.51, 104.70)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 709)
[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 722874 reads in 180.492 CPU sec, 5.710 real sec
[M::process] read 725626 sequences (100000257 bp) in 2.386 CPU sec, 2.385 real sec...
[M::mem_process_seqs] Processed 723196 reads in 126.460 CPU sec, 3.986 real sec
sorting block 16, #reads = 1110867 mem = 536876112 peak = 876724224
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 302899, 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: (130, 187, 263)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 529)
[M::mem_pestat] mean and std.dev: (203.71, 97.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 662)
[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 723208 sequences (100000243 bp) in 2.902 CPU sec, 2.979 real sec...
[M::process] read 378398 sequences (52359775 bp) in 1.370 CPU sec, 1.371 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 300651, 4, 5)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (142, 247, 806)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2134)
[M::mem_pestat] mean and std.dev: (538.73, 595.78)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2922)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (135, 196, 278)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 564)
[M::mem_pestat] mean and std.dev: (214.84, 104.37)
[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_pestat] skip orientation FF
[M::mem_process_seqs] Processed 732608 reads in 194.669 CPU sec, 6.195 real sec
sorting block 17, #reads = 1107184 mem = 536882050 peak = 876724224
[M::mem_process_seqs] Processed 725626 reads in 128.260 CPU sec, 4.110 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 299366, 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: (137, 197, 279)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 563)
[M::mem_pestat] mean and std.dev: (215.92, 104.14)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 705)
[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): (7, 156493, 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: (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: (218.12, 106.11)
[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 723208 reads in 147.834 CPU sec, 5.010 real sec
sorting block 18, #reads = 1109894 mem = 536883314 peak = 938340352
[M::mem_process_seqs] Processed 378398 reads in 73.221 CPU sec, 2.372 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: 22079414
overall: 69838409728 mem 4222.492 user 181.972 sys 153.952 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.L003\tPU:L003\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: 153.992 sec; CPU: 4404.467 sec
sorting block 19, #reads = 1079286 mem = 522088614 peak = 1025028096
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: 1227240184
output reads: 22183093
bam_mem_sort: 20 calls 9.506 user 0.055 sys 9.616 real
bam_write: 20 calls 4.959 user 0.291 sys 5.257 real
execute: 1 calls 7.285 user 0.533 sys 164.274 real
merge_files: 1 calls 7.257 user 0.513 sys 9.620 real
parse_chunk: 320 calls 16.033 user 3.690 sys 20.031 real
read_chunk: 867 calls 8.714 user 6.738 sys 98.108 real
sort_block: 1 calls 6.850 user 6.397 sys 94.968 real
write_chunk: 545 calls 6.858 user 0.263 sys 8.727 real
overall: 2257559552 mem 342.607 user 15.606 sys 164.299 real
ls: cannot access '*.cram': No such file or directory