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 1596.725 CPU sec, 57.016 real sec
[M::process] read 721906 sequences (100000160 bp) in 1.253 CPU sec, 1.256 real sec...
[M::process] read 720360 sequences (100000186 bp) in 2.076 CPU sec, 2.092 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 298989, 4, 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, 203, 290)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 592)
[M::mem_pestat] mean and std.dev: (222.78, 109.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 743)
[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 719978 sequences (100000092 bp) in 2.103 CPU sec, 2.113 real sec...
[M::process] read 717852 sequences (100000027 bp) in 1.933 CPU sec, 1.983 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 298651, 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: (140, 205, 294)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 602)
[M::mem_pestat] mean and std.dev: (225.07, 110.58)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 756)
[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 721906 reads in 215.599 CPU sec, 6.929 real sec
[M::mem_process_seqs] Processed 720360 reads in 128.195 CPU sec, 4.150 real sec
sorting block 0, #reads = 1111253 mem = 536878575 peak = 556396544
[M::process] read 720894 sequences (100000186 bp) in 2.373 CPU sec, 2.439 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 298569, 5, 4)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (140, 205, 290)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 590)
[M::mem_pestat] mean and std.dev: (223.36, 107.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 740)
[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 720038 sequences (100000097 bp) in 1.579 CPU sec, 1.584 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 297693, 3, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (142, 207, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 592)
[M::mem_pestat] mean and std.dev: (224.87, 107.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 742)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 299149, 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: (139, 205, 294)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 604)
[M::mem_pestat] mean and std.dev: (225.04, 110.84)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 759)
[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 719978 reads in 265.228 CPU sec, 8.620 real sec
[M::mem_process_seqs] Processed 717852 reads in 200.350 CPU sec, 6.582 real sec
[M::mem_process_seqs] Processed 720894 reads in 221.428 CPU sec, 7.288 real sec
sorting block 1, #reads = 1109849 mem = 536880163 peak = 688517120
[M::process] read 719846 sequences (100000000 bp) in 2.492 CPU sec, 2.591 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 298733, 5, 7)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (136, 180, 269)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 535)
[M::mem_pestat] mean and std.dev: (167.12, 57.04)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 668)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (140, 205, 294)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 602)
[M::mem_pestat] mean and std.dev: (225.46, 110.70)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 756)
[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
sorting block 2, #reads = 1110434 mem = 536877719 peak = 689348608
[M::process] read 719144 sequences (100000239 bp) in 2.291 CPU sec, 2.356 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 298295, 2, 2)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (236, 497, 738)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1742)
[M::mem_pestat] mean and std.dev: (498.50, 300.09)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2244)
[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: (222.22, 106.91)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 732)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::mem_process_seqs] Processed 720038 reads in 190.637 CPU sec, 6.088 real sec
[M::process] read 720032 sequences (100000208 bp) in 1.619 CPU sec, 1.674 real sec...
[M::mem_process_seqs] Processed 719846 reads in 136.238 CPU sec, 4.360 real sec
sorting block 3, #reads = 1110173 mem = 536878754 peak = 700272640
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 298272, 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: (141, 206, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 594)
[M::mem_pestat] mean and std.dev: (224.65, 108.38)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 745)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 719460 sequences (100000131 bp) in 2.652 CPU sec, 2.723 real sec...
[M::process] read 719536 sequences (100000057 bp) in 1.809 CPU sec, 1.808 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 298364, 5, 6)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (294, 801, 2100)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5712)
[M::mem_pestat] mean and std.dev: (1132.91, 888.96)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 7518)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (140, 205, 294)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 602)
[M::mem_pestat] mean and std.dev: (225.54, 110.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 756)
[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 719144 reads in 187.153 CPU sec, 5.969 real sec
[M::mem_process_seqs] Processed 720032 reads in 122.782 CPU sec, 3.923 real sec
sorting block 4, #reads = 1109367 mem = 536878494 peak = 700272640
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 298699, 5, 2)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (141, 205, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 597)
[M::mem_pestat] mean and std.dev: (225.11, 110.15)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 749)
[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 718962 sequences (100000291 bp) in 3.210 CPU sec, 3.400 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 297855, 2, 10)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (141, 204, 289)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 585)
[M::mem_pestat] mean and std.dev: (222.57, 107.05)
[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] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (281, 807, 807)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1859)
[M::mem_pestat] mean and std.dev: (536.22, 266.96)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2385)
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 719460 reads in 187.069 CPU sec, 6.147 real sec
sorting block 5, #reads = 1109966 mem = 536879453 peak = 715112448
[M::mem_process_seqs] Processed 719536 reads in 124.419 CPU sec, 3.946 real sec
[M::process] read 719258 sequences (100000255 bp) in 2.987 CPU sec, 3.072 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 297764, 3, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (141, 205, 291)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 591)
[M::mem_pestat] mean and std.dev: (223.68, 107.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 741)
[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 6, #reads = 1109059 mem = 536881166 peak = 715112448
[M::process] read 719536 sequences (100000050 bp) in 3.492 CPU sec, 3.672 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 298112, 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: (141, 206, 295)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 603)
[M::mem_pestat] mean and std.dev: (226.27, 110.95)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 757)
[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 718962 reads in 187.564 CPU sec, 5.993 real sec
[M::mem_process_seqs] Processed 719258 reads in 123.341 CPU sec, 3.914 real sec
[M::process] read 719382 sequences (100000205 bp) in 2.978 CPU sec, 3.093 real sec...
sorting block 7, #reads = 1109455 mem = 536878874 peak = 715112448
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 298562, 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: (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: (224.43, 109.50)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 745)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 720448 sequences (100000195 bp) in 3.152 CPU sec, 3.337 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 298541, 3, 4)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (141, 204, 289)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 585)
[M::mem_pestat] mean and std.dev: (222.92, 107.49)
[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 719536 reads in 182.978 CPU sec, 5.837 real sec
[M::mem_process_seqs] Processed 719382 reads in 124.937 CPU sec, 3.961 real sec
sorting block 8, #reads = 1109440 mem = 536878224 peak = 715112448
[M::process] read 727112 sequences (100000126 bp) in 3.579 CPU sec, 3.764 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 298016, 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: (140, 203, 288)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 584)
[M::mem_pestat] mean and std.dev: (221.92, 107.65)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 732)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 300843, 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: (134, 194, 277)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 563)
[M::mem_pestat] mean and std.dev: (214.17, 105.44)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 727714 sequences (100000052 bp) in 3.607 CPU sec, 3.816 real sec...
[M::mem_process_seqs] Processed 720448 reads in 194.654 CPU sec, 6.231 real sec
[M::mem_process_seqs] Processed 727112 reads in 133.898 CPU sec, 4.248 real sec
sorting block 9, #reads = 1109774 mem = 536878377 peak = 715112448
[M::process] read 725088 sequences (100000123 bp) in 3.441 CPU sec, 3.619 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 301767, 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: (133, 193, 275)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 559)
[M::mem_pestat] mean and std.dev: (212.46, 103.86)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 701)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
sorting block 10, #reads = 1111319 mem = 536881183 peak = 732311552
[M::process] read 729366 sequences (100000139 bp) in 3.201 CPU sec, 3.314 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 300880, 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: (135, 197, 279)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 567)
[M::mem_pestat] mean and std.dev: (215.66, 104.84)
[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::mem_process_seqs] Processed 727714 reads in 210.542 CPU sec, 6.714 real sec
[M::mem_process_seqs] Processed 725088 reads in 146.236 CPU sec, 4.624 real sec
[M::process] read 726616 sequences (100000026 bp) in 3.332 CPU sec, 3.488 real sec...
sorting block 11, #reads = 1110328 mem = 536880619 peak = 732311552
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 301710, 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: (132, 191, 271)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 549)
[M::mem_pestat] mean and std.dev: (209.71, 101.98)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 688)
[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 725680 sequences (100000021 bp) in 3.783 CPU sec, 4.000 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 300742, 2, 1)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (163, 229, 795)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2059)
[M::mem_pestat] mean and std.dev: (405.45, 298.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2691)
[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: (213.56, 104.13)
[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_pestat] skip orientation FF
[M::mem_process_seqs] Processed 729366 reads in 214.811 CPU sec, 6.838 real sec
[M::mem_process_seqs] Processed 726616 reads in 142.828 CPU sec, 4.518 real sec
[M::process] read 723754 sequences (100000067 bp) in 3.285 CPU sec, 3.425 real sec...
sorting block 12, #reads = 1108251 mem = 536878611 peak = 732311552
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 300934, 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: (135, 195, 278)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 564)
[M::mem_pestat] mean and std.dev: (214.80, 104.60)
[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 724250 sequences (100000018 bp) in 3.327 CPU sec, 3.560 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 299621, 4, 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: (216.20, 105.52)
[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 725680 reads in 210.255 CPU sec, 6.704 real sec
[M::mem_process_seqs] Processed 723754 reads in 141.519 CPU sec, 4.488 real sec
sorting block 13, #reads = 1111445 mem = 536877603 peak = 732311552
[M::process] read 724222 sequences (100000109 bp) in 3.070 CPU sec, 3.199 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 300085, 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: (136, 198, 283)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 577)
[M::mem_pestat] mean and std.dev: (218.07, 107.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 724)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
sorting block 14, #reads = 1108911 mem = 536877052 peak = 749830144
[M::process] read 722850 sequences (100000034 bp) in 3.381 CPU sec, 3.600 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (18, 299463, 1, 4)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (262, 562, 562)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1162)
[M::mem_pestat] mean and std.dev: (449.12, 192.09)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1462)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (136, 197, 281)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 571)
[M::mem_pestat] mean and std.dev: (216.84, 106.15)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 716)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::mem_process_seqs] Processed 724250 reads in 192.719 CPU sec, 6.170 real sec
[M::mem_process_seqs] Processed 724222 reads in 129.045 CPU sec, 4.081 real sec
[M::process] read 726822 sequences (100000141 bp) in 3.246 CPU sec, 3.374 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 299300, 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: (137, 198, 281)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 569)
[M::mem_pestat] mean and std.dev: (217.09, 105.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 713)
[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 15, #reads = 1112550 mem = 536879143 peak = 749830144
[M::process] read 723466 sequences (100000161 bp) in 3.028 CPU sec, 3.261 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 300939, 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: (134, 194, 274)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 554)
[M::mem_pestat] mean and std.dev: (212.28, 103.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 694)
[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 722850 reads in 196.466 CPU sec, 6.249 real sec
[M::mem_process_seqs] Processed 726822 reads in 136.270 CPU sec, 4.304 real sec
[M::process] read 719864 sequences (100000056 bp) in 3.045 CPU sec, 3.168 real sec...
sorting block 16, #reads = 1109335 mem = 536878676 peak = 749830144
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 300008, 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: (137, 199, 284)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 578)
[M::mem_pestat] mean and std.dev: (218.86, 107.43)
[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::process] read 719080 sequences (100000263 bp) in 3.067 CPU sec, 3.288 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 298189, 3, 5)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (254, 380, 1189)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3059)
[M::mem_pestat] mean and std.dev: (632.36, 478.35)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 3994)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (140, 203, 288)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 584)
[M::mem_pestat] mean and std.dev: (221.88, 106.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 732)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::process] read 88390 sequences (12266361 bp) in 0.800 CPU sec, 0.809 real sec...
[M::mem_process_seqs] Processed 723466 reads in 195.211 CPU sec, 6.264 real sec
[M::mem_process_seqs] Processed 719864 reads in 128.615 CPU sec, 4.122 real sec
sorting block 17, #reads = 1109350 mem = 536877175 peak = 749830144
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 298030, 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: (141, 203, 287)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 579)
[M::mem_pestat] mean and std.dev: (221.52, 106.05)
[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] # candidate unique pairs for (FF, FR, RF, RR): (0, 36642, 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: (140, 202, 285)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 575)
[M::mem_pestat] mean and std.dev: (220.13, 105.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 720)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 719080 reads in 112.873 CPU sec, 3.715 real sec
[M::mem_process_seqs] Processed 88390 reads in 33.667 CPU sec, 1.093 real sec
sorting block 18, #reads = 1107834 mem = 536880872 peak = 930537472
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: 21750906
overall: 69877882880 mem 4593.529 user 299.910 sys 174.263 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.L001\tPU:L001\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: 174.313 sec; CPU: 4893.453 sec
sorting block 19, #reads = 765171 mem = 370619929 peak = 930537472
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: 1204903980
output reads: 21853264
bam_mem_sort: 20 calls 10.222 user 0.088 sys 10.367 real
bam_write: 20 calls 5.737 user 0.249 sys 6.018 real
execute: 1 calls 7.149 user 0.735 sys 184.036 real
merge_files: 1 calls 7.133 user 0.698 sys 9.145 real
parse_chunk: 316 calls 15.667 user 3.937 sys 20.020 real
read_chunk: 856 calls 9.999 user 8.981 sys 113.301 real
sort_block: 1 calls 7.641 user 8.585 sys 109.658 real
write_chunk: 538 calls 6.829 user 0.510 sys 8.504 real
overall: 2145869824 mem 333.886 user 19.549 sys 184.060 real
ls: cannot access '*.cram': No such file or directory