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 1778.316 CPU sec, 65.586 real sec
[M::process] read 725322 sequences (100000135 bp) in 1.264 CPU sec, 1.267 real sec...
[M::process] read 721652 sequences (100000014 bp) in 1.671 CPU sec, 1.686 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 300470, 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: (136, 198, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 568)
[M::mem_pestat] mean and std.dev: (215.94, 104.58)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 712)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 720502 sequences (100000011 bp) in 1.409 CPU sec, 1.415 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 298445, 1, 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, 201, 286)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 582)
[M::mem_pestat] mean and std.dev: (220.42, 107.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 730)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 719174 sequences (100000053 bp) in 1.399 CPU sec, 1.413 real sec...
[M::mem_process_seqs] Processed 725322 reads in 148.645 CPU sec, 4.683 real sec
[M::mem_process_seqs] Processed 721652 reads in 93.065 CPU sec, 2.948 real sec
sorting block 0, #reads = 1112027 mem = 536882543 peak = 608268288
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 298612, 1, 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, 286)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 580)
[M::mem_pestat] mean and std.dev: (220.47, 106.21)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 727)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 726214 sequences (100000129 bp) in 2.488 CPU sec, 2.618 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 297989, 1, 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, 205, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 594)
[M::mem_pestat] mean and std.dev: (224.32, 108.79)
[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::mem_process_seqs] Processed 720502 reads in 143.872 CPU sec, 4.557 real sec
[M::process] read 722814 sequences (100000109 bp) in 1.865 CPU sec, 1.869 real sec...
[M::mem_process_seqs] Processed 719174 reads in 95.281 CPU sec, 2.995 real sec
sorting block 1, #reads = 1109854 mem = 536876581 peak = 737243136
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 300140, 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: (135, 197, 281)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 573)
[M::mem_pestat] mean and std.dev: (215.90, 105.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 719)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 721196 sequences (100000069 bp) in 1.944 CPU sec, 1.983 real sec...
[M::process] read 721014 sequences (100000204 bp) in 1.430 CPU sec, 1.425 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299350, 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: (138, 201, 287)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 585)
[M::mem_pestat] mean and std.dev: (220.63, 108.36)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 734)
[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 726214 reads in 139.242 CPU sec, 4.408 real sec
[M::mem_process_seqs] Processed 722814 reads in 91.716 CPU sec, 2.916 real sec
sorting block 2, #reads = 1111486 mem = 536879861 peak = 877195264
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 299262, 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: (139, 202, 285)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 577)
[M::mem_pestat] mean and std.dev: (220.16, 106.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 723)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 726912 sequences (100000169 bp) in 2.189 CPU sec, 2.243 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 299130, 6, 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: (221.02, 107.40)
[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 722482 sequences (100000198 bp) in 1.560 CPU sec, 1.562 real sec...
[M::mem_process_seqs] Processed 721196 reads in 141.095 CPU sec, 4.476 real sec
sorting block 3, #reads = 1113271 mem = 536879274 peak = 877195264
[M::mem_process_seqs] Processed 721014 reads in 93.521 CPU sec, 2.956 real sec
sorting block 4, #reads = 1111723 mem = 536878713 peak = 893173760
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 300631, 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: (134, 196, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 572)
[M::mem_pestat] mean and std.dev: (215.37, 105.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 718)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 721318 sequences (100000216 bp) in 2.180 CPU sec, 2.218 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 299275, 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: (138, 202, 287)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 585)
[M::mem_pestat] mean and std.dev: (220.76, 107.42)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 734)
[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 722068 sequences (100000278 bp) in 1.570 CPU sec, 1.564 real sec...
[M::mem_process_seqs] Processed 726912 reads in 142.093 CPU sec, 4.511 real sec
[M::mem_process_seqs] Processed 722482 reads in 93.381 CPU sec, 2.953 real sec
sorting block 5, #reads = 1113820 mem = 536875687 peak = 893173760
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 298846, 3, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (139, 202, 285)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 577)
[M::mem_pestat] mean and std.dev: (220.09, 106.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 723)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 726262 sequences (100000034 bp) in 2.774 CPU sec, 2.971 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 299694, 5, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (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: (220.30, 107.18)
[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 721318 reads in 145.276 CPU sec, 4.614 real sec
[M::mem_process_seqs] Processed 722068 reads in 97.602 CPU sec, 3.077 real sec
[M::process] read 723302 sequences (100000120 bp) in 1.952 CPU sec, 1.997 real sec...
sorting block 6, #reads = 1110562 mem = 536888428 peak = 893173760
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 300751, 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: (135, 197, 282)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 576)
[M::mem_pestat] mean and std.dev: (216.75, 106.61)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 723)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 721128 sequences (100000175 bp) in 2.131 CPU sec, 2.171 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299990, 5, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (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: (219.62, 107.21)
[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 723878 sequences (100000091 bp) in 1.650 CPU sec, 1.650 real sec...
[M::mem_process_seqs] Processed 726262 reads in 144.718 CPU sec, 4.596 real sec
sorting block 7, #reads = 1110614 mem = 536878558 peak = 893173760
[M::mem_process_seqs] Processed 723302 reads in 97.232 CPU sec, 3.078 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 298833, 3, 7)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (139, 201, 285)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 577)
[M::mem_pestat] mean and std.dev: (219.59, 105.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 723)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
sorting block 8, #reads = 1114042 mem = 536878469 peak = 893173760
[M::process] read 727542 sequences (100000077 bp) in 3.368 CPU sec, 3.572 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 299724, 5, 9)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (136, 197, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 568)
[M::mem_pestat] mean and std.dev: (215.98, 104.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 712)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 721128 reads in 156.333 CPU sec, 4.992 real sec
[M::mem_process_seqs] Processed 723878 reads in 106.574 CPU sec, 3.375 real sec
[M::process] read 723360 sequences (100000120 bp) in 2.269 CPU sec, 2.334 real sec...
sorting block 9, #reads = 1110831 mem = 536881552 peak = 893173760
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 300790, 3, 4)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (133, 192, 273)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 553)
[M::mem_pestat] mean and std.dev: (211.09, 102.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 693)
[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 721280 sequences (100000119 bp) in 2.246 CPU sec, 2.299 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299777, 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: (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: (218.16, 106.29)
[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 727542 reads in 161.261 CPU sec, 5.111 real sec
[M::process] read 729008 sequences (100000029 bp) in 1.820 CPU sec, 1.822 real sec...
[M::mem_process_seqs] Processed 723360 reads in 106.918 CPU sec, 3.382 real sec
sorting block 10, #reads = 1112335 mem = 536881389 peak = 893173760
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 298428, 2, 13)
[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, 200, 283)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 571)
[M::mem_pestat] mean and std.dev: (218.73, 105.08)
[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] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (61, 385, 385)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1033)
[M::mem_pestat] mean and std.dev: (222.18, 154.48)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1357)
[M::mem_pestat] skip orientation RR
[M::process] read 730688 sequences (100000282 bp) in 3.191 CPU sec, 3.404 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 301673, 6, 1)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (873, 880, 899)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (821, 951)
[M::mem_pestat] mean and std.dev: (882.00, 8.02)
[M::mem_pestat] low and high boundaries for proper pairs: (795, 977)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (133, 191, 270)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 544)
[M::mem_pestat] mean and std.dev: (208.85, 100.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 681)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::mem_process_seqs] Processed 721280 reads in 167.228 CPU sec, 5.300 real sec
[M::process] read 724992 sequences (100000153 bp) in 1.873 CPU sec, 1.879 real sec...
sorting block 11, #reads = 1110382 mem = 536878187 peak = 893173760
[M::mem_process_seqs] Processed 729008 reads in 113.683 CPU sec, 3.600 real sec
sorting block 12, #reads = 1109603 mem = 536883497 peak = 893173760
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 302322, 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: (131, 189, 268)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 542)
[M::mem_pestat] mean and std.dev: (207.57, 100.48)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 679)
[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 722166 sequences (100000007 bp) in 2.779 CPU sec, 2.823 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 299844, 4, 6)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (135, 196, 279)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 567)
[M::mem_pestat] mean and std.dev: (215.53, 105.02)
[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 731104 sequences (100000228 bp) in 2.160 CPU sec, 2.160 real sec...
[M::mem_process_seqs] Processed 730688 reads in 169.398 CPU sec, 5.353 real sec
[M::mem_process_seqs] Processed 724992 reads in 112.509 CPU sec, 3.559 real sec
sorting block 13, #reads = 1112831 mem = 536878874 peak = 893173760
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299029, 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: (138, 200, 283)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 573)
[M::mem_pestat] mean and std.dev: (218.62, 105.95)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 718)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 727030 sequences (100000129 bp) in 2.832 CPU sec, 2.895 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 301858, 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: (131, 189, 267)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 539)
[M::mem_pestat] mean and std.dev: (206.65, 99.59)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 675)
[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 724516 sequences (100000007 bp) in 1.900 CPU sec, 1.897 real sec...
[M::mem_process_seqs] Processed 722166 reads in 167.707 CPU sec, 5.313 real sec
[M::mem_process_seqs] Processed 731104 reads in 111.967 CPU sec, 3.551 real sec
sorting block 14, #reads = 1109795 mem = 536878918 peak = 893173760
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 300579, 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: (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: (213.00, 103.74)
[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 723780 sequences (100000130 bp) in 3.174 CPU sec, 3.381 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 299978, 3, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (136, 197, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 568)
[M::mem_pestat] mean and std.dev: (216.46, 104.96)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 712)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 727030 reads in 163.420 CPU sec, 5.197 real sec
[M::mem_process_seqs] Processed 724516 reads in 110.032 CPU sec, 3.476 real sec
[M::process] read 734358 sequences (100000181 bp) in 2.032 CPU sec, 2.062 real sec...
sorting block 15, #reads = 1115131 mem = 536876692 peak = 893173760
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 299428, 6, 3)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (137, 197, 280)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 566)
[M::mem_pestat] mean and std.dev: (216.33, 104.78)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 709)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
sorting block 16, #reads = 1111545 mem = 536876214 peak = 893173760
[M::process] read 728076 sequences (100000106 bp) in 2.547 CPU sec, 2.633 real sec...
[M::process] read 722478 sequences (100000160 bp) in 1.760 CPU sec, 1.759 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 303137, 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: (128, 185, 261)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 527)
[M::mem_pestat] mean and std.dev: (202.44, 97.21)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 660)
[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 723780 reads in 175.945 CPU sec, 5.592 real sec
[M::mem_process_seqs] Processed 734358 reads in 115.750 CPU sec, 3.681 real sec
sorting block 17, #reads = 1108901 mem = 536878917 peak = 893173760
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 301776, 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: (133, 193, 274)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 556)
[M::mem_pestat] mean and std.dev: (211.97, 103.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 697)
[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 436860 sequences (60584666 bp) in 2.374 CPU sec, 2.513 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 299305, 2, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (138, 200, 282)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 570)
[M::mem_pestat] mean and std.dev: (217.95, 104.48)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 714)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 728076 reads in 154.932 CPU sec, 4.984 real sec
[M::mem_process_seqs] Processed 722478 reads in 100.196 CPU sec, 3.256 real sec
sorting block 18, #reads = 1111014 mem = 536878162 peak = 893173760
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 181077, 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: (139, 202, 287)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 583)
[M::mem_pestat] mean and std.dev: (220.74, 106.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 731)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 436860 reads in 55.937 CPU sec, 1.883 real sec
sorting block 19, #reads = 1109563 mem = 536878613 peak = 1029660672
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: 22172476
overall: 69598187520 mem 4225.720 user 200.172 sys 158.423 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.L004\tPU:L004\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: 158.462 sec; CPU: 4425.895 sec
sorting block 20, #reads = 47131 mem = 22888652 peak = 1029660672
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: 1244036198
output reads: 22276461
bam_mem_sort: 21 calls 9.650 user 0.461 sys 10.140 real
bam_write: 21 calls 8.870 user 0.577 sys 9.472 real
execute: 1 calls 6.280 user 0.659 sys 166.774 real
merge_files: 1 calls 6.259 user 0.633 sys 8.241 real
parse_chunk: 321 calls 16.358 user 3.460 sys 20.039 real
read_chunk: 870 calls 7.813 user 6.165 sys 90.371 real
sort_block: 1 calls 5.959 user 5.992 sys 86.960 real
write_chunk: 547 calls 5.967 user 0.455 sys 7.647 real
overall: 2171871232 mem 305.573 user 17.008 sys 166.796 real
ls: cannot access '*.cram': No such file or directory