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 1567.279 CPU sec, 57.081 real sec
[M::process] read 720838 sequences (100000275 bp) in 1.073 CPU sec, 1.077 real sec...
[M::process] read 720294 sequences (100000011 bp) in 1.400 CPU sec, 1.402 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 298169, 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: (140, 204, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 599)
[M::mem_pestat] mean and std.dev: (224.55, 110.30)
[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 718600 sequences (100000028 bp) in 1.439 CPU sec, 1.438 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 298918, 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, 204, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 596)
[M::mem_pestat] mean and std.dev: (224.20, 109.94)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 748)
[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 718264 sequences (100000001 bp) in 1.459 CPU sec, 1.458 real sec...
[M::mem_process_seqs] Processed 720838 reads in 150.984 CPU sec, 4.745 real sec
[M::mem_process_seqs] Processed 720294 reads in 100.020 CPU sec, 3.180 real sec
sorting block 0, #reads = 1110191 mem = 536878147 peak = 611971072
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 298353, 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, 206, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 594)
[M::mem_pestat] mean and std.dev: (224.76, 108.52)
[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 720690 sequences (100000255 bp) in 2.060 CPU sec, 2.153 real sec...
[M::process] read 719674 sequences (100000278 bp) in 1.500 CPU sec, 1.502 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 297126, 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, 206, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 592)
[M::mem_pestat] mean and std.dev: (224.41, 108.03)
[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 718600 reads in 153.625 CPU sec, 4.892 real sec
[M::mem_process_seqs] Processed 718264 reads in 103.117 CPU sec, 3.301 real sec
sorting block 1, #reads = 1110311 mem = 536877863 peak = 739373056
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 298416, 0, 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, 205, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 599)
[M::mem_pestat] mean and std.dev: (224.67, 110.17)
[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 718712 sequences (100000046 bp) in 2.513 CPU sec, 2.556 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 299006, 5, 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: (141, 206, 294)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 600)
[M::mem_pestat] mean and std.dev: (225.59, 110.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 753)
[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 719388 sequences (100000049 bp) in 1.874 CPU sec, 1.882 real sec...
[M::mem_process_seqs] Processed 720690 reads in 152.392 CPU sec, 4.816 real sec
[M::mem_process_seqs] Processed 719674 reads in 100.702 CPU sec, 3.190 real sec
sorting block 2, #reads = 1109438 mem = 536877919 peak = 823848960
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 298019, 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, 206, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 594)
[M::mem_pestat] mean and std.dev: (224.71, 108.57)
[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 720092 sequences (100000219 bp) in 2.387 CPU sec, 2.481 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 297784, 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: (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: (222.73, 107.31)
[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::mem_process_seqs] Processed 718712 reads in 155.032 CPU sec, 4.930 real sec
[M::process] read 720588 sequences (100000060 bp) in 2.220 CPU sec, 2.249 real sec...
sorting block 3, #reads = 1112207 mem = 536882439 peak = 823848960
[M::mem_process_seqs] Processed 719388 reads in 102.911 CPU sec, 3.259 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 298824, 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: (140, 206, 295)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 605)
[M::mem_pestat] mean and std.dev: (225.68, 110.18)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 760)
[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 4, #reads = 1109690 mem = 536878099 peak = 837287936
[M::process] read 718784 sequences (100000004 bp) in 2.544 CPU sec, 2.695 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 298678, 7, 5)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (283, 770, 1118)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2788)
[M::mem_pestat] mean and std.dev: (600.33, 410.42)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 3623)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (140, 205, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 596)
[M::mem_pestat] mean and std.dev: (224.27, 109.57)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 748)
[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 720092 reads in 157.614 CPU sec, 5.040 real sec
[M::mem_process_seqs] Processed 720588 reads in 105.498 CPU sec, 3.334 real sec
[M::process] read 719954 sequences (100000214 bp) in 2.056 CPU sec, 2.080 real sec...
sorting block 5, #reads = 1110091 mem = 536882535 peak = 837287936
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 297618, 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: (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: (224.82, 108.68)
[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 718148 sequences (100000153 bp) in 2.423 CPU sec, 2.567 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 298207, 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: (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: (221.26, 106.37)
[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 720720 sequences (100000269 bp) in 1.630 CPU sec, 1.635 real sec...
[M::mem_process_seqs] Processed 718784 reads in 156.602 CPU sec, 4.983 real sec
[M::mem_process_seqs] Processed 719954 reads in 104.052 CPU sec, 3.317 real sec
sorting block 6, #reads = 1109384 mem = 536876240 peak = 837287936
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 297697, 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: (142, 209, 297)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 607)
[M::mem_pestat] mean and std.dev: (227.50, 110.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 762)
[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 719402 sequences (100000067 bp) in 2.377 CPU sec, 2.484 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 298303, 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: (140, 205, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 599)
[M::mem_pestat] mean and std.dev: (224.39, 109.72)
[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::mem_process_seqs] Processed 718148 reads in 155.052 CPU sec, 4.924 real sec
[M::mem_process_seqs] Processed 720720 reads in 102.982 CPU sec, 3.258 real sec
[M::process] read 719310 sequences (100000287 bp) in 2.523 CPU sec, 2.568 real sec...
sorting block 7, #reads = 1109601 mem = 536879693 peak = 837287936
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 298155, 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, 206, 294)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 600)
[M::mem_pestat] mean and std.dev: (225.58, 109.95)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 753)
[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 8, #reads = 1111371 mem = 536879960 peak = 862359552
[M::process] read 726284 sequences (100000057 bp) in 2.668 CPU sec, 2.749 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 298163, 5, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (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: (222.46, 107.10)
[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::mem_process_seqs] Processed 719402 reads in 158.366 CPU sec, 5.045 real sec
[M::process] read 724644 sequences (100000047 bp) in 1.859 CPU sec, 1.864 real sec...
[M::mem_process_seqs] Processed 719310 reads in 106.369 CPU sec, 3.365 real sec
sorting block 9, #reads = 1109857 mem = 536883489 peak = 862359552
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 300974, 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: (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: (213.37, 104.20)
[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 720976 sequences (100000131 bp) in 2.299 CPU sec, 2.407 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 299624, 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: (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: (217.46, 106.82)
[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 722528 sequences (100000009 bp) in 2.050 CPU sec, 2.047 real sec...
[M::mem_process_seqs] Processed 726284 reads in 170.629 CPU sec, 5.434 real sec
[M::mem_process_seqs] Processed 724644 reads in 111.379 CPU sec, 3.538 real sec
sorting block 10, #reads = 1110714 mem = 536880261 peak = 862359552
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 298694, 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: (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: (221.49, 107.66)
[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::process] read 727058 sequences (100000157 bp) in 3.471 CPU sec, 3.715 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 299363, 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: (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: (218.89, 106.44)
[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_process_seqs] Processed 720976 reads in 166.065 CPU sec, 5.293 real sec
[M::mem_process_seqs] Processed 722528 reads in 112.956 CPU sec, 3.583 real sec
sorting block 11, #reads = 1110156 mem = 536885505 peak = 862359552
[M::process] read 724432 sequences (100000097 bp) in 2.245 CPU sec, 2.325 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 300915, 4, 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: (134, 194, 277)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 563)
[M::mem_pestat] mean and std.dev: (213.83, 104.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[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 = 1107394 mem = 536880810 peak = 862359552
[M::process] read 720778 sequences (100000143 bp) in 2.119 CPU sec, 2.210 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (15, 300436, 4, 2)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (173, 212, 738)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1868)
[M::mem_pestat] mean and std.dev: (329.31, 261.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2433)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (136, 198, 283)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 577)
[M::mem_pestat] mean and std.dev: (218.13, 107.14)
[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] skip orientation FF
[M::process] read 724890 sequences (100000156 bp) in 1.767 CPU sec, 1.768 real sec...
[M::mem_process_seqs] Processed 727058 reads in 170.055 CPU sec, 5.409 real sec
[M::mem_process_seqs] Processed 724432 reads in 111.563 CPU sec, 3.552 real sec
sorting block 13, #reads = 1108130 mem = 536886010 peak = 862359552
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 298573, 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, 288)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 586)
[M::mem_pestat] mean and std.dev: (222.03, 108.17)
[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 724798 sequences (100000259 bp) in 2.581 CPU sec, 2.661 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 300078, 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: (135, 197, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 570)
[M::mem_pestat] mean and std.dev: (216.00, 105.70)
[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 723484 sequences (100000157 bp) in 1.804 CPU sec, 1.809 real sec...
[M::mem_process_seqs] Processed 720778 reads in 163.723 CPU sec, 5.199 real sec
[M::mem_process_seqs] Processed 724890 reads in 110.507 CPU sec, 3.514 real sec
sorting block 14, #reads = 1106810 mem = 536881117 peak = 862359552
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 300286, 4, 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, 198, 283)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 577)
[M::mem_pestat] mean and std.dev: (217.70, 106.22)
[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::process] read 723484 sequences (100000108 bp) in 2.533 CPU sec, 2.596 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 299808, 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: (137, 200, 285)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 581)
[M::mem_pestat] mean and std.dev: (219.66, 107.70)
[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] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 724798 reads in 159.135 CPU sec, 5.061 real sec
[M::process] read 728806 sequences (100000252 bp) in 1.979 CPU sec, 1.988 real sec...
[M::mem_process_seqs] Processed 723484 reads in 106.643 CPU sec, 3.364 real sec
sorting block 15, #reads = 1109270 mem = 536878279 peak = 862359552
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 299262, 5, 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: (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: (217.62, 105.97)
[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 727272 sequences (100000160 bp) in 2.592 CPU sec, 2.684 real sec...
[M::process] read 724110 sequences (100000135 bp) in 1.790 CPU sec, 1.789 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 301184, 2, 3)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (164, 781, 1325)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3647)
[M::mem_pestat] mean and std.dev: (643.78, 627.15)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4808)
[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: (212.32, 104.29)
[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::mem_pestat] skip orientation FF
[M::mem_process_seqs] Processed 723484 reads in 175.142 CPU sec, 5.570 real sec
sorting block 16, #reads = 1111718 mem = 536879185 peak = 862359552
[M::mem_process_seqs] Processed 728806 reads in 117.661 CPU sec, 3.744 real sec
sorting block 17, #reads = 1105991 mem = 536879596 peak = 928448512
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 301584, 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: (134, 194, 277)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 563)
[M::mem_pestat] mean and std.dev: (213.60, 103.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[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 451558 sequences (62450644 bp) in 1.540 CPU sec, 1.601 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299723, 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: (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: (217.57, 105.94)
[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::mem_process_seqs] Processed 727272 reads in 139.443 CPU sec, 4.509 real sec
[M::mem_process_seqs] Processed 724110 reads in 89.716 CPU sec, 2.909 real sec
sorting block 18, #reads = 1111178 mem = 536886185 peak = 928448512
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 187545, 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: (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: (218.26, 106.35)
[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 451558 reads in 49.296 CPU sec, 1.646 real sec
sorting block 19, #reads = 1109999 mem = 536879676 peak = 959987712
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: 22108560
overall: 69624913920 mem 4048.666 user 228.393 sys 151.546 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.L008\tPU:L008\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: 151.584 sec; CPU: 4277.062 sec
sorting block 20, #reads = 18994 mem = 9190633 peak = 959987712
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: 1228533152
output reads: 22212495
bam_mem_sort: 21 calls 9.166 user 0.351 sys 9.570 real
bam_write: 21 calls 7.538 user 0.466 sys 8.032 real
execute: 1 calls 5.994 user 0.415 sys 159.004 real
merge_files: 1 calls 5.963 user 0.382 sys 7.411 real
parse_chunk: 321 calls 16.060 user 3.413 sys 19.681 real
read_chunk: 869 calls 7.256 user 6.866 sys 91.353 real
sort_block: 1 calls 5.848 user 6.588 sys 88.658 real
write_chunk: 546 calls 5.579 user 0.185 sys 6.661 real
overall: 2232213504 mem 276.218 user 16.523 sys 159.026 real
ls: cannot access '*.cram': No such file or directory