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 1793.016 CPU sec, 68.939 real sec
[M::process] read 725620 sequences (100000234 bp) in 1.156 CPU sec, 1.164 real sec...
[M::process] read 721400 sequences (100000280 bp) in 1.877 CPU sec, 1.892 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 300268, 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: (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: (215.45, 104.56)
[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 719410 sequences (100000268 bp) in 1.919 CPU sec, 1.948 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 298559, 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: (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: (222.12, 108.68)
[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::mem_process_seqs] Processed 725620 reads in 179.065 CPU sec, 5.664 real sec
[M::process] read 720258 sequences (100000194 bp) in 1.887 CPU sec, 1.895 real sec...
[M::mem_process_seqs] Processed 721400 reads in 119.833 CPU sec, 3.816 real sec
sorting block 0, #reads = 1112715 mem = 536877155 peak = 584650752
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 298256, 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: (141, 204, 288)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 582)
[M::mem_pestat] mean and std.dev: (222.00, 106.03)
[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::process] read 724582 sequences (100000290 bp) in 2.739 CPU sec, 2.892 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 298297, 7, 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, 204, 288)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 584)
[M::mem_pestat] mean and std.dev: (221.78, 106.51)
[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 721144 sequences (100000012 bp) in 1.950 CPU sec, 1.955 real sec...
[M::mem_process_seqs] Processed 719410 reads in 177.255 CPU sec, 5.607 real sec
[M::mem_process_seqs] Processed 720258 reads in 121.247 CPU sec, 3.843 real sec
sorting block 1, #reads = 1109794 mem = 536878793 peak = 713625600
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 299905, 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: (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: (217.29, 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::process] read 719178 sequences (100000018 bp) in 3.053 CPU sec, 3.161 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 298605, 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: (139, 203, 291)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 595)
[M::mem_pestat] mean and std.dev: (223.41, 109.76)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 747)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 722034 sequences (100000163 bp) in 2.239 CPU sec, 2.255 real sec...
[M::mem_process_seqs] Processed 724582 reads in 174.060 CPU sec, 5.482 real sec
sorting block 2, #reads = 1110984 mem = 536888186 peak = 721481728
[M::mem_process_seqs] Processed 721144 reads in 117.459 CPU sec, 3.707 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 298257, 3, 6)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (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: (223.53, 107.41)
[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 726306 sequences (100000249 bp) in 3.054 CPU sec, 3.153 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 298584, 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: (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: (220.21, 106.51)
[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 719178 reads in 178.164 CPU sec, 5.629 real sec
[M::process] read 722818 sequences (100000093 bp) in 2.270 CPU sec, 2.272 real sec...
sorting block 3, #reads = 1110723 mem = 536875725 peak = 721481728
[M::mem_process_seqs] Processed 722034 reads in 122.195 CPU sec, 3.856 real sec
sorting block 4, #reads = 1108257 mem = 536886568 peak = 869486592
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 300132, 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: (135, 196, 279)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 567)
[M::mem_pestat] mean and std.dev: (214.89, 104.93)
[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 720944 sequences (100000152 bp) in 2.815 CPU sec, 2.979 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 299480, 1, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (138, 201, 286)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 582)
[M::mem_pestat] mean and std.dev: (220.41, 107.65)
[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 726306 reads in 181.542 CPU sec, 5.761 real sec
[M::process] read 723702 sequences (100000144 bp) in 2.040 CPU sec, 2.039 real sec...
[M::mem_process_seqs] Processed 722818 reads in 121.463 CPU sec, 3.840 real sec
sorting block 5, #reads = 1114118 mem = 536881798 peak = 869486592
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 298530, 8, 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, 203, 288)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 586)
[M::mem_pestat] mean and std.dev: (221.62, 107.13)
[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 726098 sequences (100000107 bp) in 3.691 CPU sec, 3.941 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 299412, 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: (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: (217.97, 105.94)
[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 720944 reads in 186.316 CPU sec, 5.911 real sec
[M::mem_process_seqs] Processed 723702 reads in 128.913 CPU sec, 4.069 real sec
[M::process] read 723076 sequences (100000148 bp) in 3.059 CPU sec, 3.195 real sec...
sorting block 6, #reads = 1111627 mem = 536876677 peak = 869486592
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 300260, 8, 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, 196, 279)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 567)
[M::mem_pestat] mean and std.dev: (214.82, 104.67)
[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 720154 sequences (100000047 bp) in 3.034 CPU sec, 3.249 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299634, 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: (137, 200, 286)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 584)
[M::mem_pestat] mean and std.dev: (220.11, 108.08)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 733)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 726098 reads in 182.864 CPU sec, 5.840 real sec
[M::mem_process_seqs] Processed 723076 reads in 123.008 CPU sec, 3.887 real sec
sorting block 7, #reads = 1110999 mem = 536877353 peak = 869486592
[M::process] read 725924 sequences (100000040 bp) in 3.533 CPU sec, 3.755 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 298539, 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, 205, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 596)
[M::mem_pestat] mean and std.dev: (223.80, 108.87)
[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
sorting block 8, #reads = 1113239 mem = 536880497 peak = 869486592
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 300577, 1, 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: (135, 195, 276)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 558)
[M::mem_pestat] mean and std.dev: (213.23, 102.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 699)
[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 726454 sequences (100000086 bp) in 3.504 CPU sec, 3.762 real sec...
[M::mem_process_seqs] Processed 720154 reads in 199.091 CPU sec, 6.400 real sec
[M::mem_process_seqs] Processed 725924 reads in 140.063 CPU sec, 4.464 real sec
[M::process] read 722752 sequences (100000176 bp) in 3.871 CPU sec, 4.196 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 300344, 4, 4)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (134, 194, 276)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 560)
[M::mem_pestat] mean and std.dev: (213.65, 104.43)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 702)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 726454 reads in 114.891 CPU sec, 3.851 real sec
sorting block 9, #reads = 1108710 mem = 536884076 peak = 869486592
[M::process] read 721476 sequences (100000158 bp) in 3.336 CPU sec, 3.633 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 299407, 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: (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: (218.84, 106.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 722)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 298886, 9, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (138, 200, 284)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 576)
[M::mem_pestat] mean and std.dev: (219.32, 106.34)
[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
sorting block 10, #reads = 1111462 mem = 536881494 peak = 869486592
[M::process] read 731014 sequences (100000235 bp) in 3.601 CPU sec, 3.967 real sec...
[M::mem_process_seqs] Processed 722752 reads in 218.094 CPU sec, 7.052 real sec
[M::mem_process_seqs] Processed 721476 reads in 142.905 CPU sec, 4.587 real sec
[M::process] read 727482 sequences (100000173 bp) in 3.302 CPU sec, 3.573 real sec...
sorting block 11, #reads = 1108921 mem = 536879469 peak = 869486592
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 301410, 12, 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, 193, 274)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 554)
[M::mem_pestat] mean and std.dev: (211.82, 102.57)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 694)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (2, 1472, 1745)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5231)
[M::mem_pestat] mean and std.dev: (891.42, 927.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 6974)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::process] read 722864 sequences (100000073 bp) in 3.249 CPU sec, 3.485 real sec...
[M::mem_process_seqs] Processed 727482 reads in 119.229 CPU sec, 3.871 real sec
sorting block 12, #reads = 1108627 mem = 536878470 peak = 869486592
[M::process] read 725250 sequences (100000080 bp) in 3.423 CPU sec, 3.673 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 299384, 1, 3)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (137, 198, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 566)
[M::mem_pestat] mean and std.dev: (217.06, 105.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 709)
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 301982, 3, 3)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (131, 189, 266)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 536)
[M::mem_pestat] mean and std.dev: (206.39, 99.07)
[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
[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 728648 sequences (100000265 bp) in 2.590 CPU sec, 2.631 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299965, 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: (135, 195, 276)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 558)
[M::mem_pestat] mean and std.dev: (213.60, 103.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 699)
[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 731014 reads in 434.336 CPU sec, 14.192 real sec
[M::mem_process_seqs] Processed 722864 reads in 237.438 CPU sec, 7.798 real sec
[M::mem_process_seqs] Processed 725250 reads in 171.397 CPU sec, 5.602 real sec
sorting block 13, #reads = 1108721 mem = 536883553 peak = 869486592
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 301452, 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: (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: (209.39, 100.95)
[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 725352 sequences (100000223 bp) in 4.059 CPU sec, 4.368 real sec...
[M::mem_process_seqs] Processed 728648 reads in 116.516 CPU sec, 4.462 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 300164, 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: (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: (214.04, 103.63)
[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
sorting block 14, #reads = 1108294 mem = 536876332 peak = 869486592
[M::process] read 725366 sequences (100000101 bp) in 3.661 CPU sec, 3.988 real sec...
[M::mem_process_seqs] Processed 725352 reads in 114.316 CPU sec, 4.070 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 300478, 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: (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, 104.23)
[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 731146 sequences (100000258 bp) in 3.544 CPU sec, 3.798 real sec...
[M::mem_process_seqs] Processed 725366 reads in 118.336 CPU sec, 4.025 real sec
sorting block 15, #reads = 1113917 mem = 536878422 peak = 869486592
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 301841, 3, 3)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (131, 189, 266)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 536)
[M::mem_pestat] mean and std.dev: (206.06, 99.09)
[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
[M::process] read 731286 sequences (100000079 bp) in 3.780 CPU sec, 4.083 real sec...
[M::mem_process_seqs] Processed 731146 reads in 127.874 CPU sec, 4.252 real sec
sorting block 16, #reads = 1112086 mem = 536880804 peak = 869486592
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 302321, 3, 6)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (128, 200, 821)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2207)
[M::mem_pestat] mean and std.dev: (228.62, 226.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2900)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (130, 189, 266)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 538)
[M::mem_pestat] mean and std.dev: (206.50, 99.72)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 674)
[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 731286 reads in 123.410 CPU sec, 4.084 real sec
[M::process] read 726678 sequences (100000048 bp) in 4.048 CPU sec, 4.348 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 301147, 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: (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, 104.14)
[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 687144 sequences (95038087 bp) in 3.322 CPU sec, 3.581 real sec...
sorting block 17, #reads = 1109435 mem = 536876864 peak = 869486592
[M::mem_process_seqs] Processed 726678 reads in 121.560 CPU sec, 4.515 real sec
sorting block 18, #reads = 1111319 mem = 536886002 peak = 962347008
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 284656, 8, 1)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (404, 416, 738)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1406)
[M::mem_pestat] mean and std.dev: (426.10, 239.42)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1740)
[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: (219.09, 106.96)
[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_pestat] skip orientation FF
[M::mem_process_seqs] Processed 687144 reads in 112.145 CPU sec, 4.528 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: 21695560
overall: 69961535488 mem 4850.283 user 256.806 sys 194.040 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.L006\tPU:L006\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: 194.089 sec; CPU: 5107.103 sec
sorting block 19, #reads = 692551 mem = 334794322 peak = 962347008
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: 1240926198
output reads: 21796499
bam_mem_sort: 20 calls 13.905 user 0.813 sys 14.766 real
bam_write: 20 calls 10.824 user 1.064 sys 15.706 real
execute: 1 calls 9.144 user 0.804 sys 206.329 real
merge_files: 1 calls 9.135 user 0.752 sys 11.681 real
parse_chunk: 314 calls 17.851 user 5.056 sys 24.169 real
read_chunk: 852 calls 11.483 user 7.247 sys 123.524 real
sort_block: 1 calls 8.664 user 6.784 sys 118.861 real
write_chunk: 536 calls 8.669 user 0.543 sys 10.815 real
overall: 2213584896 mem 381.887 user 24.048 sys 206.355 real
ls: cannot access '*.cram': No such file or directory