.command.log - Workdir - DAQ:SENTIEON_BWAMEM (NA12878_c_0002_gDNA_0003_B23KGCJLT4_1;L007;0001)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/0993f1d7d86e5cd335da818709ad55/.command.log
Size: 50.9 KB
Task: DAQ:SENTIEON_BWAMEM (NA12878_c_0002_gDNA_0003_B23KGCJLT4_1;L007;0001)
Attempt
Content

  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/80/0993f1d7d86e5cd335da818709ad55/.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/c7/873a3744ce7c8675cc1ee62c3ac2b2/NA12878_c_0002_gDNA_0003_B23KGCJLT4_1/NA12878_c_0002_gDNA_0003_B23KGCJLT4_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/80/0993f1d7d86e5cd335da818709ad55/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/873a3744ce7c8675cc1ee62c3ac2b2/NA12878_c_0002_gDNA_0003_B23KGCJLT4_1/NA12878_c_0002_gDNA_0003_B23KGCJLT4_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 NA12878_c_0002_gDNA_0003_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.
version: sentieon-genomics-202308.03
No more license available for sentieon:klib
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
[M::main_mem] bwa index loaded in 1664.670 CPU sec, 479.065 real sec
[M::process] read 683290 sequences (100000057 bp) in 0.899 CPU sec, 0.906 real sec...
[M::process] read 682168 sequences (100000136 bp) in 1.151 CPU sec, 1.195 real sec...
[M::process] read 680980 sequences (100000011 bp) in 1.150 CPU sec, 1.184 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 283455, 0, 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: (200, 300, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 863)
[M::mem_pestat] mean and std.dev: (320.36, 152.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1084)
[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 680398 sequences (100000007 bp) in 1.185 CPU sec, 1.201 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 282858, 2, 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: (209, 316, 440)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 902)
[M::mem_pestat] mean and std.dev: (334.96, 158.57)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1133)
[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: (241, 477, 966)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2416)
[M::mem_pestat] mean and std.dev: (573.36, 368.38)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 3141)
[M::mem_pestat] skip orientation RR
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 283558, 0, 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: (205, 309, 430)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 880)
[M::mem_pestat] mean and std.dev: (327.70, 154.67)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1105)
[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 683290 reads in 219.569 CPU sec, 7.186 real sec
[M::mem_process_seqs] Processed 680980 reads in 142.528 CPU sec, 4.723 real sec
[M::mem_process_seqs] Processed 682168 reads in 153.678 CPU sec, 5.104 real sec
sorting block 0, #reads = 1069499 mem = 536878156 peak = 597131264
[M::process] read 679982 sequences (100000090 bp) in 1.640 CPU sec, 1.813 real sec...
[M::process] read 679972 sequences (100000274 bp) in 1.222 CPU sec, 1.252 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 282160, 1, 8)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (213, 321, 450)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 924)
[M::mem_pestat] mean and std.dev: (341.49, 161.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1161)
[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 682972 sequences (100000063 bp) in 1.076 CPU sec, 1.085 real sec...
[M::mem_process_seqs] Processed 679982 reads in 73.741 CPU sec, 2.335 real sec
sorting block 1, #reads = 1069088 mem = 536886716 peak = 833101824
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (14, 282657, 0, 9)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (100, 137, 187)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 361)
[M::mem_pestat] mean and std.dev: (142.77, 46.28)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 448)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (211, 320, 448)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 922)
[M::mem_pestat] mean and std.dev: (340.29, 162.21)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1159)
[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 681986 sequences (100000017 bp) in 1.363 CPU sec, 1.366 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 282315, 0, 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: (212, 319, 449)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 923)
[M::mem_pestat] mean and std.dev: (340.99, 163.36)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1160)
[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 680398 reads in 207.651 CPU sec, 6.652 real sec
[M::mem_process_seqs] Processed 679972 reads in 95.996 CPU sec, 3.083 real sec
sorting block 2, #reads = 1068327 mem = 536881086 peak = 883576832
[M::process] read 680912 sequences (100000059 bp) in 1.530 CPU sec, 1.655 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (12, 283662, 1, 7)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (152, 261, 340)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 716)
[M::mem_pestat] mean and std.dev: (217.92, 91.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 904)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 306, 429)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 883)
[M::mem_pestat] mean and std.dev: (326.21, 156.04)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1110)
[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 680638 sequences (100000225 bp) in 1.190 CPU sec, 1.192 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 283587, 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: (207, 313, 437)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 897)
[M::mem_pestat] mean and std.dev: (331.58, 157.30)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1127)
[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 682972 reads in 131.361 CPU sec, 4.212 real sec
sorting block 3, #reads = 1068520 mem = 536879542 peak = 883576832
[M::mem_process_seqs] Processed 681986 reads in 81.680 CPU sec, 2.624 real sec
sorting block 4, #reads = 1070254 mem = 536884155 peak = 883576832
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 283258, 0, 15)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (171, 171, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 534)
[M::mem_pestat] mean and std.dev: (213.73, 80.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 655)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (211, 318, 445)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 913)
[M::mem_pestat] mean and std.dev: (337.87, 160.33)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1147)
[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: (153, 213, 321)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 657)
[M::mem_pestat] mean and std.dev: (188.50, 57.50)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 825)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::process] read 680280 sequences (100000127 bp) in 1.583 CPU sec, 1.693 real sec...
[M::process] read 680584 sequences (100000184 bp) in 1.250 CPU sec, 1.251 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 283261, 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: (211, 320, 448)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 922)
[M::mem_pestat] mean and std.dev: (340.36, 162.28)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1159)
[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 680912 reads in 133.848 CPU sec, 4.290 real sec
[M::mem_process_seqs] Processed 680638 reads in 83.618 CPU sec, 2.678 real sec
sorting block 5, #reads = 1069754 mem = 536879280 peak = 883576832
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 282556, 0, 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: (211, 319, 448)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 922)
[M::mem_pestat] mean and std.dev: (340.31, 162.47)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1159)
[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: (296, 560, 560)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1088)
[M::mem_pestat] mean and std.dev: (418.09, 158.30)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1352)
[M::mem_pestat] skip orientation RR
[M::process] read 682740 sequences (100000019 bp) in 1.661 CPU sec, 1.787 real sec...
[M::process] read 681214 sequences (100000209 bp) in 1.210 CPU sec, 1.208 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 282573, 0, 12)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (314, 314, 335)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (272, 377)
[M::mem_pestat] mean and std.dev: (326.00, 10.39)
[M::mem_pestat] low and high boundaries for proper pairs: (251, 398)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (209, 316, 447)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 923)
[M::mem_pestat] mean and std.dev: (339.07, 163.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1161)
[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: (167, 213, 368)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 770)
[M::mem_pestat] mean and std.dev: (228.75, 97.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 971)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 680280 reads in 135.983 CPU sec, 4.357 real sec
[M::mem_process_seqs] Processed 680584 reads in 84.240 CPU sec, 2.693 real sec
sorting block 6, #reads = 1068158 mem = 536880390 peak = 883576832
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 283709, 0, 3)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 307, 429)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 883)
[M::mem_pestat] mean and std.dev: (326.07, 155.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1110)
[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 680416 sequences (100000064 bp) in 1.922 CPU sec, 2.062 real sec...
[M::process] read 679790 sequences (100000301 bp) in 1.240 CPU sec, 1.232 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 283328, 2, 3)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (138, 164, 384)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 876)
[M::mem_pestat] mean and std.dev: (177.78, 79.43)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1122)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (208, 315, 438)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 898)
[M::mem_pestat] mean and std.dev: (333.64, 157.95)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1128)
[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 682740 reads in 133.147 CPU sec, 4.260 real sec
[M::mem_process_seqs] Processed 681214 reads in 82.291 CPU sec, 2.631 real sec
sorting block 7, #reads = 1069174 mem = 536879757 peak = 883576832
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (16, 282338, 1, 13)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (124, 197, 340)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 772)
[M::mem_pestat] mean and std.dev: (196.33, 82.21)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 988)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (212, 320, 447)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 917)
[M::mem_pestat] mean and std.dev: (339.37, 160.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1152)
[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: (123, 161, 238)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 468)
[M::mem_pestat] mean and std.dev: (168.73, 55.60)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 583)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::process] read 680156 sequences (100000249 bp) in 1.722 CPU sec, 1.861 real sec...
[M::process] read 680572 sequences (100000187 bp) in 1.280 CPU sec, 1.272 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 282831, 0, 3)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (215, 324, 451)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 923)
[M::mem_pestat] mean and std.dev: (343.51, 162.54)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1159)
[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 680416 reads in 134.185 CPU sec, 4.303 real sec
sorting block 8, #reads = 1069704 mem = 536880712 peak = 883576832
[M::mem_process_seqs] Processed 679790 reads in 83.528 CPU sec, 2.669 real sec
sorting block 9, #reads = 1067743 mem = 536878880 peak = 933687296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 282536, 7, 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: (211, 318, 447)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 919)
[M::mem_pestat] mean and std.dev: (339.65, 162.58)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1155)
[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 682496 sequences (100000183 bp) in 2.042 CPU sec, 2.188 real sec...
[M::process] read 681276 sequences (100000274 bp) in 1.390 CPU sec, 1.386 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 282676, 0, 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: (210, 316, 448)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 924)
[M::mem_pestat] mean and std.dev: (340.00, 165.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1162)
[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 680156 reads in 136.527 CPU sec, 4.360 real sec
[M::mem_process_seqs] Processed 680572 reads in 84.887 CPU sec, 2.707 real sec
sorting block 10, #reads = 1068516 mem = 536880279 peak = 933687296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (12, 283136, 0, 5)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (153, 309, 650)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1644)
[M::mem_pestat] mean and std.dev: (305.90, 172.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2141)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 306, 430)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 884)
[M::mem_pestat] mean and std.dev: (327.03, 156.84)
[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_pestat] skip orientation FF
[M::process] read 680130 sequences (100000170 bp) in 1.992 CPU sec, 2.160 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 282714, 0, 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: (208, 314, 442)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 910)
[M::mem_pestat] mean and std.dev: (335.24, 160.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1144)
[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 679920 sequences (100000253 bp) in 1.420 CPU sec, 1.423 real sec...
[M::mem_process_seqs] Processed 682496 reads in 134.544 CPU sec, 4.308 real sec
[M::mem_process_seqs] Processed 681276 reads in 83.711 CPU sec, 2.667 real sec
sorting block 11, #reads = 1069861 mem = 536878033 peak = 933687296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 282948, 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: (212, 320, 446)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 914)
[M::mem_pestat] mean and std.dev: (339.62, 160.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1148)
[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 680540 sequences (100000175 bp) in 2.076 CPU sec, 2.233 real sec...
[M::process] read 680832 sequences (100000069 bp) in 1.330 CPU sec, 1.329 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 281582, 0, 11)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (181, 195, 253)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (37, 397)
[M::mem_pestat] mean and std.dev: (198.80, 52.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 469)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (212, 318, 445)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 911)
[M::mem_pestat] mean and std.dev: (339.18, 161.29)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1144)
[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: (219, 253, 286)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (85, 420)
[M::mem_pestat] mean and std.dev: (225.00, 74.33)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 522)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 680130 reads in 135.947 CPU sec, 4.349 real sec
sorting block 12, #reads = 1070601 mem = 536878612 peak = 933687296
[M::mem_process_seqs] Processed 679920 reads in 85.294 CPU sec, 2.718 real sec
sorting block 13, #reads = 1067321 mem = 536878795 peak = 933687296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 282551, 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: (208, 313, 441)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 907)
[M::mem_pestat] mean and std.dev: (335.32, 160.64)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1140)
[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 684756 sequences (100000298 bp) in 1.876 CPU sec, 1.997 real sec...
[M::process] read 682800 sequences (100000067 bp) in 1.360 CPU sec, 1.366 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (14, 282739, 1, 9)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (146, 202, 253)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 467)
[M::mem_pestat] mean and std.dev: (201.43, 74.60)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 574)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (208, 314, 445)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 919)
[M::mem_pestat] mean and std.dev: (337.10, 163.10)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1156)
[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 680540 reads in 137.933 CPU sec, 4.412 real sec
[M::mem_process_seqs] Processed 680832 reads in 85.819 CPU sec, 2.730 real sec
sorting block 14, #reads = 1067918 mem = 536882377 peak = 933687296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 283958, 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: (194, 295, 422)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 878)
[M::mem_pestat] mean and std.dev: (318.97, 156.35)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1106)
[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 682482 sequences (100000293 bp) in 2.226 CPU sec, 2.380 real sec...
[M::process] read 681426 sequences (100000011 bp) in 1.340 CPU sec, 1.348 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 284014, 0, 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: (202, 307, 432)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 892)
[M::mem_pestat] mean and std.dev: (327.37, 156.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1122)
[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 684756 reads in 140.382 CPU sec, 4.476 real sec
[M::mem_process_seqs] Processed 682800 reads in 85.497 CPU sec, 2.724 real sec
sorting block 15, #reads = 1067970 mem = 536882673 peak = 933687296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (13, 284008, 0, 8)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (163, 192, 321)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 637)
[M::mem_pestat] mean and std.dev: (203.09, 75.97)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 795)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 309, 435)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 899)
[M::mem_pestat] mean and std.dev: (329.49, 157.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1131)
[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 681300 sequences (100000069 bp) in 1.905 CPU sec, 2.029 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 283598, 0, 9)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (91, 304, 1291)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3691)
[M::mem_pestat] mean and std.dev: (506.20, 520.97)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4891)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (206, 310, 431)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 881)
[M::mem_pestat] mean and std.dev: (328.79, 154.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1106)
[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 681944 sequences (100000145 bp) in 1.480 CPU sec, 1.479 real sec...
[M::mem_process_seqs] Processed 682482 reads in 139.929 CPU sec, 4.463 real sec
[M::mem_process_seqs] Processed 681426 reads in 86.726 CPU sec, 2.747 real sec
sorting block 16, #reads = 1068501 mem = 536879722 peak = 933687296
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 283315, 0, 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: (207, 310, 428)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 870)
[M::mem_pestat] mean and std.dev: (327.38, 152.58)
[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::process] read 683816 sequences (100000177 bp) in 2.162 CPU sec, 2.267 real sec...
[M::process] read 682832 sequences (100000075 bp) in 1.340 CPU sec, 1.339 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 283051, 0, 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: (203, 304, 427)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 875)
[M::mem_pestat] mean and std.dev: (325.82, 155.33)
[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 681300 reads in 135.804 CPU sec, 4.318 real sec
sorting block 17, #reads = 1066527 mem = 536879963 peak = 933687296
[M::mem_process_seqs] Processed 681944 reads in 86.620 CPU sec, 2.746 real sec
sorting block 18, #reads = 1066831 mem = 536878143 peak = 957538304
[M::process] read 682056 sequences (100000163 bp) in 1.996 CPU sec, 2.133 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 283819, 1, 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: (202, 304, 425)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 871)
[M::mem_pestat] mean and std.dev: (323.88, 153.51)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1094)
[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: (146, 496, 496)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1196)
[M::mem_pestat] mean and std.dev: (313.30, 184.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1546)
[M::mem_pestat] skip orientation RR
[M::process] read 681644 sequences (100000274 bp) in 1.350 CPU sec, 1.353 real sec...
[M::mem_process_seqs] Processed 682832 reads in 74.269 CPU sec, 2.342 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 284195, 1, 9)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (137, 191, 317)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 677)
[M::mem_pestat] mean and std.dev: (209.09, 80.64)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 857)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (198, 298, 419)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 861)
[M::mem_pestat] mean and std.dev: (318.37, 151.68)
[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::mem_pestat] skip orientation FF
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 283529, 3, 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: (205, 308, 430)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 880)
[M::mem_pestat] mean and std.dev: (327.23, 154.54)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1105)
[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 680992 sequences (100000189 bp) in 1.634 CPU sec, 1.634 real sec...
[M::mem_process_seqs] Processed 683816 reads in 210.329 CPU sec, 6.686 real sec
sorting block 19, #reads = 1066399 mem = 536878776 peak = 957538304
[M::mem_process_seqs] Processed 682056 reads in 98.637 CPU sec, 3.151 real sec
sorting block 20, #reads = 1067949 mem = 536880264 peak = 957538304
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 283182, 0, 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: (205, 309, 432)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 886)
[M::mem_pestat] mean and std.dev: (329.00, 155.81)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1113)
[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 682916 sequences (100000241 bp) in 2.360 CPU sec, 2.522 real sec...
[M::process] read 682852 sequences (100000258 bp) in 1.300 CPU sec, 1.300 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 283480, 1, 5)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (167, 190, 243)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (15, 395)
[M::mem_pestat] mean and std.dev: (192.60, 49.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (209, 315, 438)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 896)
[M::mem_pestat] mean and std.dev: (333.81, 157.72)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1125)
[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 681644 reads in 146.153 CPU sec, 4.649 real sec
[M::mem_process_seqs] Processed 680992 reads in 88.200 CPU sec, 2.804 real sec
sorting block 21, #reads = 1063168 mem = 536880979 peak = 957538304
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (14, 283838, 1, 16)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (195, 227, 232)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (121, 306)
[M::mem_pestat] mean and std.dev: (231.00, 18.67)
[M::mem_pestat] low and high boundaries for proper pairs: (84, 343)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 303, 428)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 882)
[M::mem_pestat] mean and std.dev: (325.34, 156.85)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1109)
[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: (158, 284, 298)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 578)
[M::mem_pestat] mean and std.dev: (221.38, 75.70)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 718)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::process] read 682078 sequences (100000246 bp) in 2.225 CPU sec, 2.399 real sec...
[M::process] read 681292 sequences (100000252 bp) in 1.350 CPU sec, 1.348 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 283725, 0, 19)
[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: (201, 302, 422)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 864)
[M::mem_pestat] mean and std.dev: (321.81, 152.98)
[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] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (204, 218, 327)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 573)
[M::mem_pestat] mean and std.dev: (238.94, 97.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 696)
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 682916 reads in 140.887 CPU sec, 4.477 real sec
[M::mem_process_seqs] Processed 682852 reads in 87.281 CPU sec, 2.769 real sec
sorting block 22, #reads = 1065264 mem = 536877342 peak = 957538304
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 283597, 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: (205, 307, 427)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 871)
[M::mem_pestat] mean and std.dev: (326.17, 154.07)
[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::process] read 680630 sequences (100000267 bp) in 2.245 CPU sec, 2.396 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 282969, 0, 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: (207, 311, 432)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 882)
[M::mem_pestat] mean and std.dev: (329.61, 154.62)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1107)
[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: (154, 229, 264)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 484)
[M::mem_pestat] mean and std.dev: (207.91, 78.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 594)
[M::mem_pestat] skip orientation RR
[M::process] read 680468 sequences (100000005 bp) in 1.330 CPU sec, 1.329 real sec...
[M::mem_process_seqs] Processed 682078 reads in 136.512 CPU sec, 4.339 real sec
sorting block 23, #reads = 1067186 mem = 536879816 peak = 957538304
[M::mem_process_seqs] Processed 681292 reads in 87.578 CPU sec, 2.777 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 283052, 0, 12)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (111, 127, 172)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 294)
[M::mem_pestat] mean and std.dev: (142.55, 61.81)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 390)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (210, 316, 440)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 900)
[M::mem_pestat] mean and std.dev: (335.15, 158.09)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1130)
[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: (126, 162, 265)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 543)
[M::mem_pestat] mean and std.dev: (205.42, 124.15)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 702)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
sorting block 24, #reads = 1067170 mem = 536883450 peak = 957538304
[M::process] read 683402 sequences (100000100 bp) in 2.240 CPU sec, 2.375 real sec...
[M::process] read 682528 sequences (100000299 bp) in 1.390 CPU sec, 1.392 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 282669, 0, 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: (210, 314, 439)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 897)
[M::mem_pestat] mean and std.dev: (335.01, 159.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1126)
[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: (146, 146, 191)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (56, 281)
[M::mem_pestat] mean and std.dev: (157.90, 47.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 347)
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 680630 reads in 143.660 CPU sec, 4.566 real sec
[M::mem_process_seqs] Processed 680468 reads in 91.950 CPU sec, 2.919 real sec
sorting block 25, #reads = 1063362 mem = 536878625 peak = 957538304
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 284191, 0, 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: (198, 300, 425)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 879)
[M::mem_pestat] mean and std.dev: (322.80, 156.94)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1106)
[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 681644 sequences (100000010 bp) in 2.148 CPU sec, 2.271 real sec...
[M::process] read 680850 sequences (100000032 bp) in 1.350 CPU sec, 1.349 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 284129, 0, 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: (202, 305, 430)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 886)
[M::mem_pestat] mean and std.dev: (326.14, 156.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1114)
[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 683402 reads in 141.521 CPU sec, 4.502 real sec
[M::mem_process_seqs] Processed 682528 reads in 87.320 CPU sec, 2.773 real sec
sorting block 26, #reads = 1064863 mem = 536880742 peak = 957538304
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 283132, 0, 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: (206, 313, 439)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 905)
[M::mem_pestat] mean and std.dev: (332.96, 159.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1138)
[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 680736 sequences (100000116 bp) in 2.236 CPU sec, 2.401 real sec...
[M::process] read 680668 sequences (100000206 bp) in 1.350 CPU sec, 1.350 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (13, 283379, 2, 10)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (142, 227, 689)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1783)
[M::mem_pestat] mean and std.dev: (372.15, 330.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2330)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (210, 316, 442)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 906)
[M::mem_pestat] mean and std.dev: (336.11, 159.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1138)
[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: (132, 179, 248)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 480)
[M::mem_pestat] mean and std.dev: (172.70, 57.61)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 596)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 681644 reads in 142.885 CPU sec, 4.543 real sec
[M::mem_process_seqs] Processed 680850 reads in 90.492 CPU sec, 2.870 real sec
sorting block 27, #reads = 1066951 mem = 536877977 peak = 957538304
[M::process] read 51614 sequences (7576120 bp) in 0.529 CPU sec, 0.537 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 283222, 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: (209, 312, 436)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 890)
[M::mem_pestat] mean and std.dev: (332.54, 157.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1117)
[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): (6, 282815, 0, 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: (209, 312, 437)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 893)
[M::mem_pestat] mean and std.dev: (333.65, 158.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1121)
[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: (170, 181, 213)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (84, 299)
[M::mem_pestat] mean and std.dev: (173.11, 42.77)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 344)
[M::mem_pestat] skip orientation RR
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 21501, 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: (208, 312, 444)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 916)
[M::mem_pestat] mean and std.dev: (335.68, 162.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1152)
[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 680736 reads in 139.842 CPU sec, 4.528 real sec
sorting block 28, #reads = 1064729 mem = 536878122 peak = 957538304
[M::mem_process_seqs] Processed 680668 reads in 89.222 CPU sec, 2.889 real sec
[M::mem_process_seqs] Processed 51614 reads in 90.129 CPU sec, 2.925 real sec
sorting block 29, #reads = 1065743 mem = 536882106 peak = 1096740864
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: 32081970
overall: 69610295296 mem 4904.508 user 303.854 sys 601.123 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.NA12878_c_0002_gDNA_0003_B23KGCJLT4_1.L007\tPU:L007\tSM:NA12878_c_0002_gDNA_0003_B23KGCJLT4_1\tLB:NA12878_c_0002_gDNA_0003_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 NA12878_c_0002_gDNA_0003_B23KGCJLT4_1_R1.fastq.gz NA12878_c_0002_gDNA_0003_B23KGCJLT4_1_R2.fastq.gz
[main] Real time: 601.159 sec; CPU: 5208.364 sec
sorting block 30, #reads = 210469 mem = 106090487 peak = 1096740864
uniq header count 1
merging 31 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: 1741337238
output reads: 32237520
bam_mem_sort: 31 calls 11.588 user 0.170 sys 11.837 real
bam_write: 31 calls 9.094 user 0.341 sys 9.518 real
execute: 1 calls 6.157 user 0.329 sys 610.242 real
merge_files: 1 calls 6.124 user 0.317 sys 8.975 real
parse_chunk: 484 calls 16.261 user 4.375 sys 20.955 real
read_chunk: 1307 calls 11.091 user 10.984 sys 117.458 real
sort_block: 1 calls 8.905 user 10.412 sys 114.079 real
write_chunk: 821 calls 5.756 user 0.166 sys 8.260 real
overall: 2352168960 mem 338.859 user 21.322 sys 610.263 real
ls: cannot access '*.cram': No such file or directory