Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/e25e953263897b7a493db795f8c014/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/41fb5f91cb15aca830d42a5e1095ed/659_cuO-T1-TDNA-1_A23MHWWLT4_1/659_cuO-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/e25e953263897b7a493db795f8c014/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/41fb5f91cb15aca830d42a5e1095ed/659_cuO-T1-TDNA-1_A23MHWWLT4_1/659_cuO-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz ==> STAGING COMPLETE (7 inputs) 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 1490.697 CPU sec, 53.078 real sec [M::process] read 725690 sequences (100000185 bp) in 1.104 CPU sec, 1.115 real sec... [M::process] read 721948 sequences (100000087 bp) in 1.688 CPU sec, 1.683 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 299955, 4, 4) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (84, 135, 581) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1575) [M::mem_pestat] mean and std.dev: (309.10, 268.85) [M::mem_pestat] low and high boundaries for proper pairs: (1, 2072) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (135, 196, 278) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 564) [M::mem_pestat] mean and std.dev: (214.60, 103.57) [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::mem_pestat] skip orientation FF [M::process] read 717822 sequences (100000192 bp) in 1.530 CPU sec, 1.529 real sec... [M::process] read 717472 sequences (100000229 bp) in 1.636 CPU sec, 1.673 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299165, 1, 3) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (139, 202, 287) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 583) [M::mem_pestat] mean and std.dev: (220.91, 107.12) [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 725690 reads in 173.192 CPU sec, 5.474 real sec [M::mem_process_seqs] Processed 721948 reads in 110.080 CPU sec, 3.517 real sec sorting block 0, #reads = 1113381 mem = 536878349 peak = 600469504 [M::process] read 724830 sequences (100000154 bp) in 2.142 CPU sec, 2.194 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 297980, 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: (142, 206, 292) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 592) [M::mem_pestat] mean and std.dev: (225.19, 108.39) [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::process] read 721766 sequences (100000036 bp) in 1.601 CPU sec, 1.612 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 299314, 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: (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: (215.87, 104.52) [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_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 297306, 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: (142, 208, 294) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 598) [M::mem_pestat] mean and std.dev: (226.05, 108.73) [M::mem_pestat] low and high boundaries for proper pairs: (1, 750) [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 717822 reads in 230.381 CPU sec, 7.384 real sec [M::mem_process_seqs] Processed 724830 reads in 176.408 CPU sec, 5.701 real sec sorting block 1, #reads = 1109376 mem = 536878860 peak = 729444352 [M::mem_process_seqs] Processed 717472 reads in 194.806 CPU sec, 6.295 real sec [M::process] read 718276 sequences (100000178 bp) in 2.389 CPU sec, 2.490 real sec... sorting block 2, #reads = 1112505 mem = 536878858 peak = 754524160 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 298576, 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, 202, 290) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 592) [M::mem_pestat] mean and std.dev: (222.57, 109.29) [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 718408 sequences (100000066 bp) in 2.006 CPU sec, 2.026 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 298186, 1, 3) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (142, 207, 294) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 598) [M::mem_pestat] mean and std.dev: (225.97, 109.41) [M::mem_pestat] low and high boundaries for proper pairs: (1, 750) [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 721766 reads in 155.878 CPU sec, 4.946 real sec [M::mem_process_seqs] Processed 718276 reads in 102.784 CPU sec, 3.237 real sec [M::process] read 725066 sequences (100000205 bp) in 2.108 CPU sec, 2.152 real sec... sorting block 3, #reads = 1110604 mem = 536877756 peak = 754524160 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 297779, 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: (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: (224.54, 108.04) [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 721374 sequences (100000129 bp) in 2.151 CPU sec, 2.207 real sec... [M::process] read 719880 sequences (100000015 bp) in 1.497 CPU sec, 1.501 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 300448, 2, 1) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (136, 197, 279) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 565) [M::mem_pestat] mean and std.dev: (215.26, 103.73) [M::mem_pestat] low and high boundaries for proper pairs: (1, 708) [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 718408 reads in 160.474 CPU sec, 5.095 real sec [M::mem_process_seqs] Processed 725066 reads in 103.577 CPU sec, 3.288 real sec sorting block 4, #reads = 1109569 mem = 536876527 peak = 754524160 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 298910, 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: (139, 202, 289) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 589) [M::mem_pestat] mean and std.dev: (221.89, 108.37) [M::mem_pestat] low and high boundaries for proper pairs: (1, 739) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::process] read 718834 sequences (100000039 bp) in 2.342 CPU sec, 2.407 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 298438, 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: (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: (222.24, 107.35) [M::mem_pestat] low and high boundaries for proper pairs: (1, 732) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::process] read 724620 sequences (100000106 bp) in 2.028 CPU sec, 2.032 real sec... [M::mem_process_seqs] Processed 721374 reads in 155.363 CPU sec, 4.910 real sec sorting block 5, #reads = 1111489 mem = 536877665 peak = 754524160 [M::mem_process_seqs] Processed 719880 reads in 111.484 CPU sec, 3.537 real sec sorting block 6, #reads = 1110336 mem = 536879374 peak = 819601408 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 297600, 5, 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, 205, 291) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 591) [M::mem_pestat] mean and std.dev: (223.79, 107.72) [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] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (145, 857, 1105) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3025) [M::mem_pestat] mean and std.dev: (712.20, 517.50) [M::mem_pestat] low and high boundaries for proper pairs: (1, 3985) [M::mem_pestat] skip orientation RR [M::process] read 721678 sequences (100000172 bp) in 2.462 CPU sec, 2.511 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 299351, 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: (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: (216.07, 104.55) [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 721182 sequences (100000202 bp) in 2.136 CPU sec, 2.140 real sec... [M::mem_process_seqs] Processed 718834 reads in 162.193 CPU sec, 5.127 real sec [M::mem_process_seqs] Processed 724620 reads in 109.707 CPU sec, 3.464 real sec sorting block 7, #reads = 1109312 mem = 536878798 peak = 819601408 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299080, 12, 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: (139, 202, 289) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 589) [M::mem_pestat] mean and std.dev: (221.91, 108.62) [M::mem_pestat] low and high boundaries for proper pairs: (1, 739) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (781, 781, 875) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (593, 1063) [M::mem_pestat] mean and std.dev: (791.44, 29.54) [M::mem_pestat] low and high boundaries for proper pairs: (499, 1157) [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_pestat] skip orientation RF [M::process] read 719584 sequences (100000244 bp) in 2.404 CPU sec, 2.473 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 298880, 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: (139, 201, 284) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 574) [M::mem_pestat] mean and std.dev: (219.28, 105.55) [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 730450 sequences (100000243 bp) in 1.780 CPU sec, 1.777 real sec... [M::mem_process_seqs] Processed 721678 reads in 161.881 CPU sec, 5.205 real sec [M::mem_process_seqs] Processed 721182 reads in 103.705 CPU sec, 3.369 real sec sorting block 8, #reads = 1113065 mem = 536878787 peak = 819601408 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 297771, 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: (140, 203, 287) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 581) [M::mem_pestat] mean and std.dev: (221.64, 106.25) [M::mem_pestat] low and high boundaries for proper pairs: (1, 728) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::process] read 726586 sequences (100000172 bp) in 2.461 CPU sec, 2.527 real sec... [M::process] read 722726 sequences (100000014 bp) in 1.781 CPU sec, 1.790 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 302060, 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: (131, 189, 265) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 533) [M::mem_pestat] mean and std.dev: (206.01, 98.67) [M::mem_pestat] low and high boundaries for proper pairs: (1, 667) [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 719584 reads in 170.282 CPU sec, 5.481 real sec sorting block 9, #reads = 1111114 mem = 536879496 peak = 819601408 [M::mem_process_seqs] Processed 730450 reads in 113.619 CPU sec, 3.608 real sec sorting block 10, #reads = 1112882 mem = 536877564 peak = 876724224 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 300862, 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: (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: (212.18, 102.89) [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::process] read 724304 sequences (100000056 bp) in 2.736 CPU sec, 2.810 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 299550, 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: (138, 200, 284) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 576) [M::mem_pestat] mean and std.dev: (219.25, 107.26) [M::mem_pestat] low and high boundaries for proper pairs: (1, 722) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::process] read 729656 sequences (100000078 bp) in 2.249 CPU sec, 2.249 real sec... [M::mem_process_seqs] Processed 726586 reads in 168.643 CPU sec, 5.332 real sec [M::mem_process_seqs] Processed 722726 reads in 113.339 CPU sec, 3.690 real sec sorting block 11, #reads = 1113777 mem = 536877284 peak = 876724224 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 299816, 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: (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: (216.09, 104.59) [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 [M::process] read 725576 sequences (100000217 bp) in 2.333 CPU sec, 2.404 real sec... [M::process] read 721750 sequences (100000281 bp) in 1.765 CPU sec, 1.766 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 301383, 2, 8) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (132, 190, 268) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 540) [M::mem_pestat] mean and std.dev: (208.05, 100.02) [M::mem_pestat] low and high boundaries for proper pairs: (1, 676) [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 724304 reads in 187.588 CPU sec, 6.064 real sec [M::mem_process_seqs] Processed 729656 reads in 126.844 CPU sec, 4.151 real sec sorting block 12, #reads = 1107440 mem = 536879385 peak = 876724224 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 300808, 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, 195, 278) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 564) [M::mem_pestat] mean and std.dev: (214.59, 104.47) [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 728014 sequences (100000149 bp) in 2.649 CPU sec, 2.720 real sec... [M::process] read 726012 sequences (100000282 bp) in 1.998 CPU sec, 2.000 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299362, 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: (138, 200, 285) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 579) [M::mem_pestat] mean and std.dev: (219.98, 107.42) [M::mem_pestat] low and high boundaries for proper pairs: (1, 726) [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 725576 reads in 187.344 CPU sec, 6.049 real sec sorting block 13, #reads = 1109680 mem = 536877334 peak = 876724224 [M::mem_process_seqs] Processed 721750 reads in 120.844 CPU sec, 3.930 real sec sorting block 14, #reads = 1109515 mem = 536881303 peak = 876724224 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 300836, 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, 191, 271) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 547) [M::mem_pestat] mean and std.dev: (209.54, 100.83) [M::mem_pestat] low and high boundaries for proper pairs: (1, 685) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::process] read 722874 sequences (100000007 bp) in 2.681 CPU sec, 2.761 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 301112, 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: (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: (214.66, 104.86) [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 723196 sequences (100000055 bp) in 1.990 CPU sec, 1.990 real sec... [M::mem_process_seqs] Processed 728014 reads in 184.703 CPU sec, 5.954 real sec [M::mem_process_seqs] Processed 726012 reads in 120.895 CPU sec, 3.837 real sec sorting block 15, #reads = 1111817 mem = 536878548 peak = 876724224 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 299721, 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: (137, 200, 284) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 578) [M::mem_pestat] mean and std.dev: (219.20, 107.06) [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 732608 sequences (100000069 bp) in 2.969 CPU sec, 3.028 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 298972, 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: (137, 198, 280) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 566) [M::mem_pestat] mean and std.dev: (216.51, 104.70) [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 [M::mem_process_seqs] Processed 722874 reads in 180.492 CPU sec, 5.710 real sec [M::process] read 725626 sequences (100000257 bp) in 2.386 CPU sec, 2.385 real sec... [M::mem_process_seqs] Processed 723196 reads in 126.460 CPU sec, 3.986 real sec sorting block 16, #reads = 1110867 mem = 536876112 peak = 876724224 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 302899, 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: (130, 187, 263) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 529) [M::mem_pestat] mean and std.dev: (203.71, 97.41) [M::mem_pestat] low and high boundaries for proper pairs: (1, 662) [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 723208 sequences (100000243 bp) in 2.902 CPU sec, 2.979 real sec... [M::process] read 378398 sequences (52359775 bp) in 1.370 CPU sec, 1.371 real sec... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 300651, 4, 5) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (142, 247, 806) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2134) [M::mem_pestat] mean and std.dev: (538.73, 595.78) [M::mem_pestat] low and high boundaries for proper pairs: (1, 2922) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (135, 196, 278) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 564) [M::mem_pestat] mean and std.dev: (214.84, 104.37) [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::mem_pestat] skip orientation FF [M::mem_process_seqs] Processed 732608 reads in 194.669 CPU sec, 6.195 real sec sorting block 17, #reads = 1107184 mem = 536882050 peak = 876724224 [M::mem_process_seqs] Processed 725626 reads in 128.260 CPU sec, 4.110 real sec [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 299366, 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: (137, 197, 279) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 563) [M::mem_pestat] mean and std.dev: (215.92, 104.14) [M::mem_pestat] low and high boundaries for proper pairs: (1, 705) [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): (7, 156493, 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: (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: (218.12, 106.11) [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 723208 reads in 147.834 CPU sec, 5.010 real sec sorting block 18, #reads = 1109894 mem = 536883314 peak = 938340352 [M::mem_process_seqs] Processed 378398 reads in 73.221 CPU sec, 2.372 real sec os version: Linux 6.12.88 cpu vendor: GenuineIntel signature: 000c06f2 features: bfebfbff 7ffefbff extended: f3bfb7ef fb417ffe amd bits: 2c100800 00000121 brand: INTEL(R) XEON(R) PLATINUM 8559C threads: 31 algo: bwa-mem license: sentieon:klib=31 reads: 22079414 overall: 69838409728 mem 4222.492 user 181.972 sys 153.952 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.L003\tPU:L003\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: 153.992 sec; CPU: 4404.467 sec sorting block 19, #reads = 1079286 mem = 522088614 peak = 1025028096 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: 1227240184 output reads: 22183093 bam_mem_sort: 20 calls 9.506 user 0.055 sys 9.616 real bam_write: 20 calls 4.959 user 0.291 sys 5.257 real execute: 1 calls 7.285 user 0.533 sys 164.274 real merge_files: 1 calls 7.257 user 0.513 sys 9.620 real parse_chunk: 320 calls 16.033 user 3.690 sys 20.031 real read_chunk: 867 calls 8.714 user 6.738 sys 98.108 real sort_block: 1 calls 6.850 user 6.397 sys 94.968 real write_chunk: 545 calls 6.858 user 0.263 sys 8.727 real overall: 2257559552 mem 342.607 user 15.606 sys 164.299 real ls: cannot access '*.cram': No such file or directory