cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o 659_wQ-N1-BDNA-1_B23KGCJLT4_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.
No more license available for sentieon:klib
version: sentieon-genomics-202308.03
No more license available for sentieon:klib
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
[M::main_mem] bwa index loaded in 1615.740 CPU sec, 535.650 real sec
[M::process] read 688182 sequences (100000300 bp) in 0.951 CPU sec, 0.957 real sec...
[M::process] read 686776 sequences (100000230 bp) in 1.150 CPU sec, 1.148 real sec...
[M::process] read 686658 sequences (100000295 bp) in 1.210 CPU sec, 1.207 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284359, 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: (189, 285, 407)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 843)
[M::mem_pestat] mean and std.dev: (308.86, 152.40)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1061)
[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 685672 sequences (100000005 bp) in 1.110 CPU sec, 1.118 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284674, 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: (193, 292, 416)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 862)
[M::mem_pestat] mean and std.dev: (315.47, 155.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1085)
[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): (1, 284397, 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: (193, 291, 418)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 868)
[M::mem_pestat] mean and std.dev: (316.63, 157.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1093)
[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 688182 reads in 203.662 CPU sec, 6.501 real sec
[M::mem_process_seqs] Processed 686776 reads in 131.783 CPU sec, 4.242 real sec
[M::mem_process_seqs] Processed 686658 reads in 143.162 CPU sec, 4.630 real sec
sorting block 0, #reads = 1091732 mem = 536879233 peak = 602279936
[M::process] read 685092 sequences (100000112 bp) in 1.659 CPU sec, 1.798 real sec...
[M::process] read 686828 sequences (100000150 bp) in 1.208 CPU sec, 1.226 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 283812, 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: (196, 295, 420)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 868)
[M::mem_pestat] mean and std.dev: (319.24, 156.82)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1092)
[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 685092 reads in 67.823 CPU sec, 2.126 real sec
[M::process] read 687980 sequences (100000141 bp) in 1.127 CPU sec, 1.128 real sec...
sorting block 1, #reads = 1089678 mem = 536880311 peak = 915447808
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 284005, 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: (195, 293, 419)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 867)
[M::mem_pestat] mean and std.dev: (318.41, 157.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1091)
[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, 284332, 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: (192, 290, 416)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 864)
[M::mem_pestat] mean and std.dev: (315.15, 156.61)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1088)
[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 687590 sequences (100000052 bp) in 1.342 CPU sec, 1.344 real sec...
[M::mem_process_seqs] Processed 685672 reads in 190.527 CPU sec, 6.043 real sec
[M::mem_process_seqs] Processed 686828 reads in 91.040 CPU sec, 2.896 real sec
sorting block 2, #reads = 1088598 mem = 536878453 peak = 915447808
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284953, 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: (190, 288, 413)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 859)
[M::mem_pestat] mean and std.dev: (311.98, 155.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1082)
[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 686454 sequences (100000265 bp) in 1.606 CPU sec, 1.709 real sec...
[M::process] read 685628 sequences (100000129 bp) in 1.190 CPU sec, 1.192 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 284363, 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: (191, 292, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 881)
[M::mem_pestat] mean and std.dev: (317.45, 159.54)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1111)
[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 687980 reads in 120.068 CPU sec, 3.818 real sec
sorting block 3, #reads = 1089984 mem = 536878971 peak = 915447808
[M::mem_process_seqs] Processed 687590 reads in 76.445 CPU sec, 2.433 real sec
sorting block 4, #reads = 1091601 mem = 536877172 peak = 915447808
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284290, 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: (194, 296, 425)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 887)
[M::mem_pestat] mean and std.dev: (320.63, 159.61)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1118)
[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 685694 sequences (100000241 bp) in 1.828 CPU sec, 1.945 real sec...
[M::process] read 688458 sequences (100000211 bp) in 1.190 CPU sec, 1.189 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 284033, 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: (195, 294, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 873)
[M::mem_pestat] mean and std.dev: (319.18, 157.82)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1099)
[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 686454 reads in 121.734 CPU sec, 3.866 real sec
[M::mem_process_seqs] Processed 685628 reads in 77.438 CPU sec, 2.464 real sec
sorting block 5, #reads = 1089912 mem = 536879430 peak = 915447808
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 283821, 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: (195, 294, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 873)
[M::mem_pestat] mean and std.dev: (319.43, 158.65)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1099)
[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 687340 sequences (100000019 bp) in 1.677 CPU sec, 1.799 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 285083, 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: (188, 286, 411)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 857)
[M::mem_pestat] mean and std.dev: (310.15, 153.93)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1080)
[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 686762 sequences (100000217 bp) in 1.280 CPU sec, 1.275 real sec...
[M::mem_process_seqs] Processed 685694 reads in 122.449 CPU sec, 3.902 real sec
[M::mem_process_seqs] Processed 688458 reads in 78.253 CPU sec, 2.483 real sec
sorting block 6, #reads = 1088650 mem = 536879698 peak = 915447808
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284168, 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: (193, 293, 419)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 871)
[M::mem_pestat] mean and std.dev: (316.64, 156.86)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1097)
[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 685450 sequences (100000217 bp) in 1.989 CPU sec, 2.115 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284012, 1, 11)
[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: (195, 296, 425)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 885)
[M::mem_pestat] mean and std.dev: (320.55, 159.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1115)
[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: (744, 744, 744)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (744, 744)
[M::mem_pestat] mean and std.dev: (744.00, 0.00)
[M::mem_pestat] low and high boundaries for proper pairs: (744, 744)
[M::mem_pestat] skip orientation RR
[M::process] read 685364 sequences (100000181 bp) in 1.310 CPU sec, 1.308 real sec...
[M::mem_process_seqs] Processed 687340 reads in 122.987 CPU sec, 3.911 real sec
[M::mem_process_seqs] Processed 686762 reads in 78.974 CPU sec, 2.503 real sec
sorting block 7, #reads = 1090558 mem = 536883383 peak = 931008512
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 283591, 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: (198, 302, 432)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 900)
[M::mem_pestat] mean and std.dev: (325.89, 160.62)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1134)
[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 686490 sequences (100000114 bp) in 1.709 CPU sec, 1.817 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 283825, 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: (196, 296, 425)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 883)
[M::mem_pestat] mean and std.dev: (321.66, 159.10)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1112)
[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 687388 sequences (100000200 bp) in 1.230 CPU sec, 1.233 real sec...
[M::mem_process_seqs] Processed 685450 reads in 123.426 CPU sec, 3.935 real sec
sorting block 8, #reads = 1090226 mem = 536879293 peak = 931008512
[M::mem_process_seqs] Processed 685364 reads in 78.369 CPU sec, 2.486 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 284186, 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: (193, 292, 416)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 862)
[M::mem_pestat] mean and std.dev: (315.92, 156.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1085)
[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 9, #reads = 1088671 mem = 536878529 peak = 931008512
[M::process] read 687270 sequences (100000300 bp) in 2.028 CPU sec, 2.167 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 284060, 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: (191, 288, 408)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 842)
[M::mem_pestat] mean and std.dev: (309.79, 150.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1059)
[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 686382 sequences (100000076 bp) in 1.270 CPU sec, 1.268 real sec...
[M::mem_process_seqs] Processed 686490 reads in 122.582 CPU sec, 3.895 real sec
[M::mem_process_seqs] Processed 687388 reads in 77.836 CPU sec, 2.463 real sec
sorting block 10, #reads = 1090221 mem = 536882532 peak = 931008512
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 284221, 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: (192, 292, 417)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 867)
[M::mem_pestat] mean and std.dev: (314.98, 155.25)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1092)
[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 685398 sequences (100000094 bp) in 1.749 CPU sec, 1.865 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 283848, 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: (195, 298, 426)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 888)
[M::mem_pestat] mean and std.dev: (321.29, 158.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1119)
[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 685476 sequences (100000016 bp) in 1.289 CPU sec, 1.298 real sec...
[M::mem_process_seqs] Processed 687270 reads in 122.914 CPU sec, 3.914 real sec
[M::mem_process_seqs] Processed 686382 reads in 78.937 CPU sec, 2.502 real sec
sorting block 11, #reads = 1090933 mem = 536884056 peak = 931008512
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 283138, 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: (198, 301, 428)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 888)
[M::mem_pestat] mean and std.dev: (324.17, 159.30)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1118)
[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 689156 sequences (100000111 bp) in 2.123 CPU sec, 2.261 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 283652, 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: (196, 296, 423)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 877)
[M::mem_pestat] mean and std.dev: (320.82, 158.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1104)
[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 689498 sequences (100000032 bp) in 1.350 CPU sec, 1.345 real sec...
[M::mem_process_seqs] Processed 685398 reads in 125.594 CPU sec, 3.988 real sec
[M::mem_process_seqs] Processed 685476 reads in 79.969 CPU sec, 2.531 real sec
sorting block 12, #reads = 1088888 mem = 536881095 peak = 931008512
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 285212, 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: (185, 279, 403)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 839)
[M::mem_pestat] mean and std.dev: (305.45, 152.85)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1057)
[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 688822 sequences (100000015 bp) in 1.803 CPU sec, 1.924 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 285158, 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: (185, 279, 404)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 842)
[M::mem_pestat] mean and std.dev: (305.65, 153.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1061)
[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 687218 sequences (100000111 bp) in 1.350 CPU sec, 1.349 real sec...
[M::mem_process_seqs] Processed 689156 reads in 129.536 CPU sec, 4.125 real sec
sorting block 13, #reads = 1088925 mem = 536877039 peak = 931008512
[M::mem_process_seqs] Processed 689498 reads in 81.964 CPU sec, 2.596 real sec
sorting block 14, #reads = 1089592 mem = 536877403 peak = 981557248
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 285576, 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: (187, 283, 408)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 850)
[M::mem_pestat] mean and std.dev: (308.42, 154.05)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1071)
[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 685754 sequences (100000054 bp) in 2.121 CPU sec, 2.238 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 284775, 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: (191, 288, 412)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 854)
[M::mem_pestat] mean and std.dev: (312.48, 154.16)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1075)
[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 688970 sequences (100000062 bp) in 1.370 CPU sec, 1.375 real sec...
[M::mem_process_seqs] Processed 688822 reads in 132.328 CPU sec, 4.201 real sec
[M::mem_process_seqs] Processed 687218 reads in 84.537 CPU sec, 2.686 real sec
sorting block 15, #reads = 1089137 mem = 536877908 peak = 981557248
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 283878, 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: (195, 292, 413)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 849)
[M::mem_pestat] mean and std.dev: (314.44, 152.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1067)
[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 690514 sequences (100000148 bp) in 1.936 CPU sec, 2.069 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 285038, 4, 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: (186, 279, 399)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 825)
[M::mem_pestat] mean and std.dev: (303.24, 149.61)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1038)
[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 689434 sequences (100000069 bp) in 1.354 CPU sec, 1.362 real sec...
[M::mem_process_seqs] Processed 685754 reads in 134.771 CPU sec, 4.293 real sec
[M::mem_process_seqs] Processed 688970 reads in 86.165 CPU sec, 2.729 real sec
sorting block 16, #reads = 1086339 mem = 536880566 peak = 981557248
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 286049, 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: (182, 275, 395)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 821)
[M::mem_pestat] mean and std.dev: (299.45, 149.05)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1034)
[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 688216 sequences (100000277 bp) in 2.080 CPU sec, 2.208 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 286058, 4, 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: (185, 280, 401)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 833)
[M::mem_pestat] mean and std.dev: (304.16, 150.79)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1049)
[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 686316 sequences (100000111 bp) in 1.380 CPU sec, 1.376 real sec...
[M::mem_process_seqs] Processed 690514 reads in 131.986 CPU sec, 4.195 real sec
[M::mem_process_seqs] Processed 689434 reads in 83.051 CPU sec, 2.628 real sec
sorting block 17, #reads = 1088245 mem = 536878616 peak = 981557248
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284918, 2, 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: (188, 285, 407)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 845)
[M::mem_pestat] mean and std.dev: (308.92, 152.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1064)
[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 18, #reads = 1089342 mem = 536878962 peak = 981557248
[M::process] read 687232 sequences (100000062 bp) in 1.915 CPU sec, 2.037 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 285020, 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: (193, 292, 415)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 859)
[M::mem_pestat] mean and std.dev: (314.60, 153.96)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1081)
[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 690214 sequences (100000267 bp) in 1.360 CPU sec, 1.360 real sec...
[M::mem_process_seqs] Processed 688216 reads in 133.459 CPU sec, 4.249 real sec
[M::mem_process_seqs] Processed 686316 reads in 84.429 CPU sec, 2.675 real sec
sorting block 19, #reads = 1088114 mem = 536878847 peak = 981557248
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 284620, 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: (190, 287, 410)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 850)
[M::mem_pestat] mean and std.dev: (311.39, 154.10)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1070)
[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 688822 sequences (100000028 bp) in 2.196 CPU sec, 2.307 real sec...
[M::process] read 687882 sequences (100000117 bp) in 1.360 CPU sec, 1.364 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 285074, 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: (183, 276, 396)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 822)
[M::mem_pestat] mean and std.dev: (299.98, 148.40)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1035)
[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 687232 reads in 137.408 CPU sec, 4.367 real sec
[M::mem_process_seqs] Processed 690214 reads in 84.689 CPU sec, 2.687 real sec
sorting block 20, #reads = 1086338 mem = 536879409 peak = 981557248
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284768, 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: (187, 282, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 832)
[M::mem_pestat] mean and std.dev: (304.48, 148.82)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1047)
[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 (100000248 bp) in 2.061 CPU sec, 2.190 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 285288, 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: (189, 285, 404)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 834)
[M::mem_pestat] mean and std.dev: (306.92, 148.96)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1049)
[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 687072 sequences (100000004 bp) in 1.390 CPU sec, 1.385 real sec...
[M::mem_process_seqs] Processed 688822 reads in 133.610 CPU sec, 4.253 real sec
[M::mem_process_seqs] Processed 687882 reads in 85.039 CPU sec, 2.688 real sec
sorting block 21, #reads = 1089215 mem = 536877611 peak = 981557248
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 284972, 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: (191, 287, 407)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 839)
[M::mem_pestat] mean and std.dev: (309.10, 149.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1055)
[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 690734 sequences (100000223 bp) in 2.324 CPU sec, 2.450 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 284688, 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: (191, 289, 411)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 851)
[M::mem_pestat] mean and std.dev: (312.11, 153.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1071)
[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 690344 sequences (100000085 bp) in 1.380 CPU sec, 1.379 real sec...
[M::mem_process_seqs] Processed 687144 reads in 136.823 CPU sec, 4.349 real sec
sorting block 22, #reads = 1088407 mem = 536878855 peak = 981557248
[M::mem_process_seqs] Processed 687072 reads in 86.871 CPU sec, 2.753 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 286223, 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: (182, 273, 395)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 821)
[M::mem_pestat] mean and std.dev: (298.58, 148.90)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1034)
[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 23, #reads = 1087708 mem = 536880795 peak = 981557248
[M::process] read 689168 sequences (100000188 bp) in 1.998 CPU sec, 2.120 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 285665, 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: (183, 278, 399)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 831)
[M::mem_pestat] mean and std.dev: (301.60, 149.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1047)
[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 687820 sequences (100000148 bp) in 1.360 CPU sec, 1.364 real sec...
[M::mem_process_seqs] Processed 690734 reads in 139.953 CPU sec, 4.460 real sec
[M::mem_process_seqs] Processed 690344 reads in 86.750 CPU sec, 2.750 real sec
sorting block 24, #reads = 1088071 mem = 536879305 peak = 981557248
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 285097, 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: (186, 283, 406)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 846)
[M::mem_pestat] mean and std.dev: (306.80, 151.67)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1066)
[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 686862 sequences (100000041 bp) in 2.208 CPU sec, 2.316 real sec...
[M::process] read 316876 sequences (46141252 bp) in 0.810 CPU sec, 0.804 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 284793, 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: (189, 285, 406)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 840)
[M::mem_pestat] mean and std.dev: (307.83, 149.90)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1057)
[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 689168 reads in 136.109 CPU sec, 4.348 real sec
[M::mem_process_seqs] Processed 687820 reads in 85.655 CPU sec, 2.740 real sec
sorting block 25, #reads = 1089218 mem = 536878932 peak = 981557248
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 284189, 0, 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: (192, 290, 409)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 843)
[M::mem_pestat] mean and std.dev: (310.96, 150.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1060)
[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, 131065, 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: (192, 288, 408)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 840)
[M::mem_pestat] mean and std.dev: (311.07, 151.38)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1056)
[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 686862 reads in 101.849 CPU sec, 3.315 real sec
[M::mem_process_seqs] Processed 316876 reads in 46.321 CPU sec, 1.503 real sec
sorting block 26, #reads = 1087366 mem = 536878649 peak = 1067741184
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 29878400
overall: 69657145344 mem 4452.374 user 250.790 sys 642.261 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:B23KGCJLT4.659_wQ-N1-BDNA-1_B23KGCJLT4_1.L008\tPU:L008\tSM:659_wQ-N1-BDNA-1_B23KGCJLT4_1\tLB:659_wQ-N1-BDNA-1_B23KGCJLT4_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_wQ-N1-BDNA-1_B23KGCJLT4_1_R1.fastq.gz 659_wQ-N1-BDNA-1_B23KGCJLT4_1_R2.fastq.gz
[main] Real time: 642.300 sec; CPU: 4703.167 sec
sorting block 27, #reads = 612098 mem = 302558985 peak = 1067741184
uniq header count 1
merging 28 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  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: 1628928430
output reads: 30017767
bam_mem_sort: 28 calls 10.589 user 0.150 sys 10.784 real
bam_write: 28 calls 16.985 user 0.362 sys 17.577 real
execute: 1 calls 5.594 user 0.357 sys 651.164 real
merge_files: 1 calls 5.584 user 0.328 sys 8.257 real
parse_chunk: 442 calls 14.108 user 3.658 sys 18.131 real
read_chunk: 1192 calls 10.542 user 10.183 sys 102.650 real
sort_block: 1 calls 8.940 user 9.708 sys 99.783 real
write_chunk: 748 calls 5.270 user 0.212 sys 7.638 real
overall: 2328592384 mem 310.751 user 19.351 sys 651.189 real
ls: cannot access '*.cram': No such file or directory