This software is licensed to bgold@natera.com by Sentieon Inc.
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.
version: sentieon-genomics-202308.03
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
[M::main_mem] bwa index loaded in 1879.270 CPU sec, 66.502 real sec
[M::process] read 723610 sequences (100000053 bp) in 1.232 CPU sec, 1.232 real sec...
[M::process] read 720724 sequences (100000164 bp) in 1.652 CPU sec, 1.770 real sec...
[M::process] read 719746 sequences (100000183 bp) in 1.665 CPU sec, 1.671 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 299412, 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: (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: (217.90, 105.46)
[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 718244 sequences (100000190 bp) in 1.338 CPU sec, 1.341 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 298372, 9, 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: (139, 203, 287)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 583)
[M::mem_pestat] mean and std.dev: (221.16, 106.79)
[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_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 298008, 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: (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: (221.66, 106.24)
[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 723610 reads in 265.647 CPU sec, 8.575 real sec
[M::mem_process_seqs] Processed 720724 reads in 174.637 CPU sec, 5.638 real sec
[M::mem_process_seqs] Processed 719746 reads in 191.209 CPU sec, 6.196 real sec
sorting block 0, #reads = 1112788 mem = 536878767 peak = 582225920
[M::process] read 723676 sequences (100000070 bp) in 2.601 CPU sec, 2.755 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 297635, 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: (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: (224.56, 107.76)
[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 721268 sequences (100000153 bp) in 1.905 CPU sec, 1.910 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (12, 299582, 4, 5)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (169, 562, 562)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1348)
[M::mem_pestat] mean and std.dev: (372.45, 198.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1741)
[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: (217.81, 105.53)
[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_pestat] skip orientation FF
[M::mem_process_seqs] Processed 718244 reads in 172.055 CPU sec, 5.487 real sec
sorting block 1, #reads = 1110125 mem = 536879294 peak = 853819392
[M::mem_process_seqs] Processed 723676 reads in 110.272 CPU sec, 3.474 real sec
[M::process] read 720934 sequences (100000292 bp) in 2.075 CPU sec, 2.146 real sec...
sorting block 2, #reads = 1111221 mem = 536880018 peak = 858935296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 298582, 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: (139, 203, 288)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 586)
[M::mem_pestat] mean and std.dev: (221.72, 107.77)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 735)
[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 719270 sequences (100000296 bp) in 2.542 CPU sec, 2.661 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 298716, 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: (139, 202, 286)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 580)
[M::mem_pestat] mean and std.dev: (220.48, 106.35)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 727)
[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 723282 sequences (100000282 bp) in 1.669 CPU sec, 1.678 real sec...
[M::mem_process_seqs] Processed 721268 reads in 174.564 CPU sec, 5.550 real sec
[M::mem_process_seqs] Processed 720934 reads in 109.493 CPU sec, 3.475 real sec
sorting block 3, #reads = 1111792 mem = 536884507 peak = 858935296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 297967, 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: (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: (223.36, 107.79)
[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 720304 sequences (100000006 bp) in 2.270 CPU sec, 2.410 real sec...
[M::process] read 719960 sequences (100000270 bp) in 1.560 CPU sec, 1.557 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 299991, 4, 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: (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: (218.60, 105.76)
[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::mem_process_seqs] Processed 719270 reads in 170.003 CPU sec, 5.415 real sec
[M::mem_process_seqs] Processed 723282 reads in 116.690 CPU sec, 3.728 real sec
sorting block 4, #reads = 1110720 mem = 536886220 peak = 858935296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 298268, 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: (140, 204, 289)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 587)
[M::mem_pestat] mean and std.dev: (222.91, 107.97)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 736)
[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 719076 sequences (100000121 bp) in 2.367 CPU sec, 2.490 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 298195, 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: (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: (221.95, 107.20)
[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 724044 sequences (100000042 bp) in 1.930 CPU sec, 1.937 real sec...
[M::mem_process_seqs] Processed 720304 reads in 167.335 CPU sec, 5.318 real sec
sorting block 5, #reads = 1111471 mem = 536879187 peak = 858935296
[M::mem_process_seqs] Processed 719960 reads in 108.027 CPU sec, 3.616 real sec
sorting block 6, #reads = 1110195 mem = 536878438 peak = 858935296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 297917, 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, 290)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 588)
[M::mem_pestat] mean and std.dev: (223.11, 107.42)
[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 722172 sequences (100000297 bp) in 2.520 CPU sec, 2.651 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299480, 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: (136, 198, 282)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 574)
[M::mem_pestat] mean and std.dev: (216.99, 105.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 720)
[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 720892 sequences (100000073 bp) in 1.840 CPU sec, 1.842 real sec...
[M::mem_process_seqs] Processed 719076 reads in 174.237 CPU sec, 5.727 real sec
[M::mem_process_seqs] Processed 724044 reads in 109.578 CPU sec, 3.484 real sec
sorting block 7, #reads = 1110488 mem = 536877483 peak = 858935296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 299307, 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, 286)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 582)
[M::mem_pestat] mean and std.dev: (220.37, 106.99)
[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 718320 sequences (100000138 bp) in 2.744 CPU sec, 2.890 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 298759, 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, 202, 286)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 580)
[M::mem_pestat] mean and std.dev: (220.52, 106.28)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 727)
[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 728260 sequences (100000173 bp) in 1.750 CPU sec, 1.749 real sec...
[M::mem_process_seqs] Processed 722172 reads in 167.061 CPU sec, 5.313 real sec
[M::mem_process_seqs] Processed 720892 reads in 107.653 CPU sec, 3.651 real sec
sorting block 8, #reads = 1112330 mem = 536878680 peak = 858935296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 297884, 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: (142, 206, 291)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 589)
[M::mem_pestat] mean and std.dev: (224.27, 107.81)
[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 724488 sequences (100000095 bp) in 2.655 CPU sec, 2.798 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 301121, 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: (133, 192, 271)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 547)
[M::mem_pestat] mean and std.dev: (209.88, 101.54)
[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 722372 sequences (100000240 bp) in 2.001 CPU sec, 2.011 real sec...
[M::mem_process_seqs] Processed 718320 reads in 172.124 CPU sec, 5.694 real sec
sorting block 9, #reads = 1111533 mem = 536881857 peak = 858935296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 300167, 1, 1)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (209, 836, 2189)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6149)
[M::mem_pestat] mean and std.dev: (1024.70, 843.40)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 8129)
[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: (216.63, 106.29)
[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_pestat] skip orientation FF
[M::process] read 721328 sequences (100000227 bp) in 2.154 CPU sec, 2.158 real sec...
[M::mem_process_seqs] Processed 724488 reads in 96.131 CPU sec, 3.039 real sec
sorting block 10, #reads = 1110269 mem = 536879503 peak = 858935296
[M::mem_process_seqs] Processed 728260 reads in 232.165 CPU sec, 7.352 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299048, 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: (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: (218.80, 106.02)
[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::process] read 730902 sequences (100000109 bp) in 2.993 CPU sec, 3.119 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 298795, 5, 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, 285)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 577)
[M::mem_pestat] mean and std.dev: (219.89, 106.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 723)
[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 722372 reads in 192.588 CPU sec, 6.132 real sec
[M::process] read 726012 sequences (100000068 bp) in 1.990 CPU sec, 2.017 real sec...
sorting block 11, #reads = 1112418 mem = 536877930 peak = 858935296
[M::mem_process_seqs] Processed 721328 reads in 120.925 CPU sec, 3.837 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 302374, 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: (131, 188, 266)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 536)
[M::mem_pestat] mean and std.dev: (206.09, 99.10)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 671)
[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 12, #reads = 1109268 mem = 536880814 peak = 858935296
[M::process] read 722566 sequences (100000163 bp) in 2.443 CPU sec, 2.688 real sec...
[M::process] read 725018 sequences (100000196 bp) in 1.819 CPU sec, 1.820 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 300659, 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: (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: (214.18, 104.19)
[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::mem_process_seqs] Processed 730902 reads in 180.223 CPU sec, 5.735 real sec
[M::mem_process_seqs] Processed 726012 reads in 115.556 CPU sec, 3.669 real sec
sorting block 13, #reads = 1113386 mem = 536882180 peak = 858935296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299328, 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: (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: (218.15, 105.93)
[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 726788 sequences (100000002 bp) in 2.573 CPU sec, 2.695 real sec...
[M::process] read 724176 sequences (100000118 bp) in 1.772 CPU sec, 1.779 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 299830, 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: (135, 196, 277)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 561)
[M::mem_pestat] mean and std.dev: (214.29, 103.80)
[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::mem_process_seqs] Processed 722566 reads in 182.346 CPU sec, 6.056 real sec
[M::mem_process_seqs] Processed 725018 reads in 117.159 CPU sec, 3.717 real sec
sorting block 14, #reads = 1109760 mem = 536882027 peak = 858935296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 300837, 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: (134, 194, 276)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 560)
[M::mem_pestat] mean and std.dev: (212.94, 103.41)
[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::process] read 721836 sequences (100000123 bp) in 2.776 CPU sec, 2.908 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 300419, 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: (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: (216.77, 105.89)
[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::process] read 728270 sequences (100000078 bp) in 1.748 CPU sec, 1.750 real sec...
[M::mem_process_seqs] Processed 726788 reads in 174.885 CPU sec, 5.658 real sec
[M::mem_process_seqs] Processed 724176 reads in 112.637 CPU sec, 3.673 real sec
sorting block 15, #reads = 1110970 mem = 536879968 peak = 858935296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299202, 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, 283)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 573)
[M::mem_pestat] mean and std.dev: (218.68, 105.67)
[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] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (124, 206, 1000)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2752)
[M::mem_pestat] mean and std.dev: (276.50, 281.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 3628)
[M::mem_pestat] skip orientation RR
[M::process] read 729740 sequences (100000225 bp) in 2.757 CPU sec, 2.880 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 301199, 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: (133, 192, 270)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 544)
[M::mem_pestat] mean and std.dev: (209.29, 100.54)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 681)
[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 724076 sequences (100000241 bp) in 1.830 CPU sec, 1.829 real sec...
[M::mem_process_seqs] Processed 721836 reads in 184.096 CPU sec, 5.965 real sec
sorting block 16, #reads = 1111467 mem = 536880498 peak = 863936512
[M::mem_process_seqs] Processed 728270 reads in 120.602 CPU sec, 3.919 real sec
sorting block 17, #reads = 1106861 mem = 536878402 peak = 980840448
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 301705, 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: (132, 189, 267)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 537)
[M::mem_pestat] mean and std.dev: (207.07, 99.52)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 672)
[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 720748 sequences (100000012 bp) in 2.740 CPU sec, 2.861 real sec...
[M::process] read 46384 sequences (6428858 bp) in 0.400 CPU sec, 0.397 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 299968, 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: (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: (215.86, 104.74)
[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 729740 reads in 177.780 CPU sec, 5.778 real sec
[M::mem_process_seqs] Processed 724076 reads in 113.190 CPU sec, 3.629 real sec
sorting block 18, #reads = 1111936 mem = 536883318 peak = 980840448
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 299204, 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: (139, 201, 285)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 577)
[M::mem_pestat] mean and std.dev: (220.34, 106.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 723)
[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, 19248, 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: (139, 202, 284)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 574)
[M::mem_pestat] mean and std.dev: (219.12, 104.87)
[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::mem_process_seqs] Processed 46384 reads in 24.595 CPU sec, 0.795 real sec
[M::mem_process_seqs] Processed 720748 reads in 99.724 CPU sec, 3.563 real sec
sorting block 19, #reads = 1108289 mem = 536879497 peak = 980840448
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 22458486
overall: 69793939456 mem 4570.221 user 287.690 sys 170.054 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.L002\tPU:L002\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: 170.087 sec; CPU: 4857.915 sec
sorting block 20, #reads = 345877 mem = 167507961 peak = 980840448
uniq header count 1
merging 21 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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: 1228703133
output reads: 22563164
bam_mem_sort: 21 calls 12.661 user 0.465 sys 13.134 real
bam_write: 21 calls 6.498 user 0.423 sys 7.494 real
execute: 1 calls 6.760 user 0.782 sys 178.393 real
merge_files: 1 calls 6.730 user 0.766 sys 8.079 real
parse_chunk: 325 calls 13.803 user 3.593 sys 17.657 real
read_chunk: 882 calls 7.884 user 7.928 sys 97.594 real
sort_block: 1 calls 5.430 user 7.537 sys 93.978 real
write_chunk: 555 calls 6.367 user 0.630 sys 7.454 real
overall: 2179280896 mem 298.404 user 19.623 sys 178.412 real
ls: cannot access '*.cram': No such file or directory