.command.log - Workdir - DAQ:SENTIEON_BWAMEM (NA12878_c_0002_gDNA_0004_B23KGCJLT4_1;L005;0001)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/534d6ecc754cb2fe50ea672c285469/.command.log
Size: 56.9 KB
Task: DAQ:SENTIEON_BWAMEM (NA12878_c_0002_gDNA_0004_B23KGCJLT4_1;L005;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/34/534d6ecc754cb2fe50ea672c285469/.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/52/3955aa90ac119b73f923abaf1d2e4e/NA12878_c_0002_gDNA_0004_B23KGCJLT4_1/NA12878_c_0002_gDNA_0004_B23KGCJLT4_1_R1.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/34/534d6ecc754cb2fe50ea672c285469/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/3955aa90ac119b73f923abaf1d2e4e/NA12878_c_0002_gDNA_0004_B23KGCJLT4_1/NA12878_c_0002_gDNA_0004_B23KGCJLT4_1_R2.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_0004_B23KGCJLT4_1.bam --sam2bam -
This software is licensed to bgold@natera.com by Sentieon Inc.
This software is licensed to bgold@natera.com by Sentieon Inc.
No more license available for sentieon:klib
version: sentieon-genomics-202308.03
No more license available for sentieon:klib
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
[M::main_mem] bwa index loaded in 1739.620 CPU sec, 599.798 real sec
[M::process] read 684740 sequences (100000263 bp) in 0.906 CPU sec, 0.913 real sec...
[M::process] read 683332 sequences (100000067 bp) in 1.110 CPU sec, 1.112 real sec...
[M::process] read 683750 sequences (100000297 bp) in 1.140 CPU sec, 1.138 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 285018, 6, 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: (200, 303, 422)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 866)
[M::mem_pestat] mean and std.dev: (320.86, 152.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1088)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 683740 sequences (100000216 bp) in 1.098 CPU sec, 1.096 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 284574, 0, 2)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (144, 144, 193)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (46, 291)
[M::mem_pestat] mean and std.dev: (155.10, 26.67)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 340)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 307, 431)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 887)
[M::mem_pestat] mean and std.dev: (326.91, 156.24)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1115)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] 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): (4, 284493, 0, 13)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (207, 312, 433)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 885)
[M::mem_pestat] mean and std.dev: (329.40, 155.57)
[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] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (256, 303, 336)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 496)
[M::mem_pestat] mean and std.dev: (253.45, 75.39)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 576)
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 684740 reads in 204.384 CPU sec, 6.549 real sec
[M::mem_process_seqs] Processed 683750 reads in 133.899 CPU sec, 4.334 real sec
[M::mem_process_seqs] Processed 683332 reads in 144.980 CPU sec, 4.711 real sec
sorting block 0, #reads = 1071510 mem = 536879084 peak = 590761984
[M::process] read 683544 sequences (100000016 bp) in 1.732 CPU sec, 1.840 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 283955, 0, 12)
[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, 305, 428)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 878)
[M::mem_pestat] mean and std.dev: (325.07, 154.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1103)
[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: (165, 197, 289)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 537)
[M::mem_pestat] mean and std.dev: (208.18, 65.85)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 661)
[M::mem_pestat] skip orientation RR
[M::process] read 683138 sequences (100000037 bp) in 1.195 CPU sec, 1.214 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (12, 284055, 2, 8)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (172, 248, 348)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 700)
[M::mem_pestat] mean and std.dev: (225.20, 78.59)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 876)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 306, 428)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 878)
[M::mem_pestat] mean and std.dev: (325.50, 154.88)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1103)
[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 683740 reads in 125.773 CPU sec, 3.997 real sec
[M::process] read 683082 sequences (100000079 bp) in 1.078 CPU sec, 1.078 real sec...
sorting block 1, #reads = 1070824 mem = 536878426 peak = 885133312
[M::mem_process_seqs] Processed 683544 reads in 79.054 CPU sec, 2.495 real sec
sorting block 2, #reads = 1071888 mem = 536880750 peak = 902262784
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 283939, 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: (205, 306, 428)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 874)
[M::mem_pestat] mean and std.dev: (326.26, 155.11)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1097)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 683912 sequences (100000151 bp) in 1.695 CPU sec, 1.823 real sec...
[M::process] read 683168 sequences (100000289 bp) in 1.190 CPU sec, 1.188 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 284084, 1, 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: (203, 303, 426)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 872)
[M::mem_pestat] mean and std.dev: (324.89, 156.04)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1095)
[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 683138 reads in 124.709 CPU sec, 3.969 real sec
[M::mem_process_seqs] Processed 683082 reads in 78.335 CPU sec, 2.493 real sec
sorting block 3, #reads = 1072280 mem = 536878066 peak = 902262784
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 284138, 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: (202, 306, 427)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 877)
[M::mem_pestat] mean and std.dev: (324.33, 153.81)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1102)
[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: (189, 193, 329)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 609)
[M::mem_pestat] mean and std.dev: (218.36, 77.74)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 749)
[M::mem_pestat] skip orientation RR
[M::process] read 683642 sequences (100000087 bp) in 1.742 CPU sec, 1.836 real sec...
[M::process] read 684074 sequences (100000036 bp) in 1.130 CPU sec, 1.135 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 283891, 1, 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: (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: (331.12, 156.75)
[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 683912 reads in 123.616 CPU sec, 3.932 real sec
[M::mem_process_seqs] Processed 683168 reads in 78.149 CPU sec, 2.488 real sec
sorting block 4, #reads = 1071111 mem = 536875262 peak = 902262784
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 283767, 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: (204, 309, 434)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 894)
[M::mem_pestat] mean and std.dev: (329.30, 157.93)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1124)
[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 683486 sequences (100000131 bp) in 1.698 CPU sec, 1.828 real sec...
[M::process] read 683838 sequences (100000095 bp) in 1.190 CPU sec, 1.187 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (13, 283945, 0, 10)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (155, 158, 2965)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8585)
[M::mem_pestat] mean and std.dev: (801.62, 1185.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 11395)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 303, 426)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 876)
[M::mem_pestat] mean and std.dev: (323.75, 154.97)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1101)
[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: (251, 328, 328)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (97, 482)
[M::mem_pestat] mean and std.dev: (255.38, 68.17)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 559)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 683642 reads in 125.301 CPU sec, 3.992 real sec
sorting block 5, #reads = 1071190 mem = 536879085 peak = 902262784
[M::mem_process_seqs] Processed 684074 reads in 79.280 CPU sec, 2.519 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 284073, 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: (204, 305, 428)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 876)
[M::mem_pestat] mean and std.dev: (325.69, 154.90)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1100)
[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 = 1071195 mem = 536885650 peak = 902262784
[M::process] read 683856 sequences (100000187 bp) in 1.962 CPU sec, 2.090 real sec...
[M::process] read 683954 sequences (100000077 bp) in 1.190 CPU sec, 1.194 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 284838, 0, 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: (201, 301, 425)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 873)
[M::mem_pestat] mean and std.dev: (323.17, 155.59)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1097)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (113, 168, 253)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 533)
[M::mem_pestat] mean and std.dev: (165.89, 56.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 673)
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 683486 reads in 126.056 CPU sec, 4.005 real sec
[M::mem_process_seqs] Processed 683838 reads in 79.683 CPU sec, 2.531 real sec
sorting block 7, #reads = 1071170 mem = 536880518 peak = 902262784
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 284694, 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: (201, 302, 427)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 879)
[M::mem_pestat] mean and std.dev: (324.24, 156.87)
[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] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (159, 210, 276)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 510)
[M::mem_pestat] mean and std.dev: (189.89, 70.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 627)
[M::mem_pestat] skip orientation RR
[M::process] read 682556 sequences (100000010 bp) in 1.756 CPU sec, 1.862 real sec...
[M::process] read 683152 sequences (100000200 bp) in 1.240 CPU sec, 1.237 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 284814, 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: (203, 307, 428)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 878)
[M::mem_pestat] mean and std.dev: (324.99, 153.82)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1103)
[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 683856 reads in 125.807 CPU sec, 4.003 real sec
[M::mem_process_seqs] Processed 683954 reads in 78.693 CPU sec, 2.496 real sec
sorting block 8, #reads = 1071406 mem = 536882991 peak = 902262784
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 283719, 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: (209, 318, 442)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 908)
[M::mem_pestat] mean and std.dev: (335.53, 158.79)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1141)
[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 683150 sequences (100000102 bp) in 2.034 CPU sec, 2.177 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 283449, 1, 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, 312, 436)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 896)
[M::mem_pestat] mean and std.dev: (330.88, 157.31)
[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] skip orientation RR as there are not enough pairs
[M::process] read 682710 sequences (100000008 bp) in 1.240 CPU sec, 1.246 real sec...
[M::mem_process_seqs] Processed 682556 reads in 124.928 CPU sec, 3.968 real sec
[M::mem_process_seqs] Processed 683152 reads in 79.871 CPU sec, 2.536 real sec
sorting block 9, #reads = 1071773 mem = 536881965 peak = 902262784
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 284910, 1, 6)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (181, 721, 2522)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7204)
[M::mem_pestat] mean and std.dev: (1484.09, 1329.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9545)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (204, 308, 430)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 882)
[M::mem_pestat] mean and std.dev: (327.24, 155.48)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1108)
[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 683720 sequences (100000296 bp) in 1.873 CPU sec, 2.011 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 284091, 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: (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: (327.59, 155.69)
[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 683568 sequences (100000020 bp) in 1.270 CPU sec, 1.266 real sec...
[M::mem_process_seqs] Processed 683150 reads in 125.067 CPU sec, 3.982 real sec
sorting block 10, #reads = 1070173 mem = 536883945 peak = 902262784
[M::mem_process_seqs] Processed 682710 reads in 78.964 CPU sec, 2.499 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 284446, 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: (202, 303, 426)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 874)
[M::mem_pestat] mean and std.dev: (324.69, 156.58)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1098)
[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 11, #reads = 1071164 mem = 536879619 peak = 925073408
[M::process] read 683452 sequences (100000174 bp) in 2.154 CPU sec, 2.309 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (18, 284715, 1, 10)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (115, 191, 242)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 496)
[M::mem_pestat] mean and std.dev: (194.00, 94.78)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 623)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 304, 429)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 883)
[M::mem_pestat] mean and std.dev: (326.30, 157.80)
[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] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (130, 211, 302)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 646)
[M::mem_pestat] mean and std.dev: (201.00, 81.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 818)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::process] read 682398 sequences (100000280 bp) in 1.260 CPU sec, 1.262 real sec...
[M::mem_process_seqs] Processed 683720 reads in 125.955 CPU sec, 4.001 real sec
[M::mem_process_seqs] Processed 683568 reads in 79.936 CPU sec, 2.532 real sec
sorting block 12, #reads = 1071643 mem = 536879841 peak = 925073408
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 284017, 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: (204, 308, 430)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 882)
[M::mem_pestat] mean and std.dev: (327.21, 155.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1108)
[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 682764 sequences (100000115 bp) in 1.885 CPU sec, 2.007 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 283686, 2, 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: (208, 315, 439)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 901)
[M::mem_pestat] mean and std.dev: (333.92, 159.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1132)
[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 683452 reads in 124.477 CPU sec, 3.966 real sec
[M::process] read 683326 sequences (100000299 bp) in 1.312 CPU sec, 1.320 real sec...
[M::mem_process_seqs] Processed 682398 reads in 79.755 CPU sec, 2.519 real sec
sorting block 13, #reads = 1071856 mem = 536879314 peak = 925073408
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 283732, 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: (207, 312, 437)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 897)
[M::mem_pestat] mean and std.dev: (331.76, 158.12)
[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::process] read 683368 sequences (100000190 bp) in 2.179 CPU sec, 2.299 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 284304, 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: (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: (324.96, 155.47)
[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 682764 reads in 124.516 CPU sec, 3.953 real sec
[M::process] read 683814 sequences (100000158 bp) in 1.310 CPU sec, 1.319 real sec...
[M::mem_process_seqs] Processed 683326 reads in 79.308 CPU sec, 2.509 real sec
sorting block 14, #reads = 1071166 mem = 536878556 peak = 925073408
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 284690, 1, 13)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 301, 424)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 870)
[M::mem_pestat] mean and std.dev: (322.94, 155.46)
[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] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (174, 191, 287)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 513)
[M::mem_pestat] mean and std.dev: (195.75, 72.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 626)
[M::mem_pestat] skip orientation RR
sorting block 15, #reads = 1071276 mem = 536880055 peak = 925073408
[M::process] read 684348 sequences (100000087 bp) in 1.965 CPU sec, 2.077 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 284150, 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: (200, 299, 422)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 866)
[M::mem_pestat] mean and std.dev: (321.40, 155.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1088)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 683368 reads in 125.854 CPU sec, 4.011 real sec
[M::process] read 685248 sequences (100000226 bp) in 1.413 CPU sec, 1.436 real sec...
[M::mem_process_seqs] Processed 683814 reads in 80.336 CPU sec, 2.534 real sec
sorting block 16, #reads = 1071323 mem = 536880780 peak = 925073408
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 284648, 2, 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: (199, 298, 424)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 874)
[M::mem_pestat] mean and std.dev: (322.01, 156.85)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1099)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 683712 sequences (100000268 bp) in 2.183 CPU sec, 2.328 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 285468, 0, 7)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (133, 165, 238)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 448)
[M::mem_pestat] mean and std.dev: (168.09, 57.44)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 553)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (198, 301, 426)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 882)
[M::mem_pestat] mean and std.dev: (322.38, 156.66)
[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 684988 sequences (100000251 bp) in 1.317 CPU sec, 1.328 real sec...
[M::mem_process_seqs] Processed 684348 reads in 131.468 CPU sec, 4.180 real sec
[M::mem_process_seqs] Processed 685248 reads in 83.501 CPU sec, 2.640 real sec
sorting block 17, #reads = 1071432 mem = 536880054 peak = 925073408
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 284283, 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: (204, 310, 436)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 900)
[M::mem_pestat] mean and std.dev: (329.87, 158.24)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1132)
[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 684826 sequences (100000034 bp) in 1.971 CPU sec, 2.074 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 285512, 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: (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: (321.18, 155.01)
[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 684560 sequences (100000227 bp) in 1.320 CPU sec, 1.322 real sec...
[M::mem_process_seqs] Processed 683712 reads in 135.113 CPU sec, 4.310 real sec
[M::mem_process_seqs] Processed 684988 reads in 84.796 CPU sec, 2.683 real sec
sorting block 18, #reads = 1071203 mem = 536878834 peak = 925073408
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 284846, 4, 2)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (168, 245, 915)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2409)
[M::mem_pestat] mean and std.dev: (501.55, 379.38)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 3156)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (198, 297, 415)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 849)
[M::mem_pestat] mean and std.dev: (316.48, 150.02)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1066)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::process] read 683994 sequences (100000123 bp) in 2.317 CPU sec, 2.415 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 285063, 0, 9)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (107, 174, 841)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2309)
[M::mem_pestat] mean and std.dev: (377.60, 351.36)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 3043)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (199, 297, 414)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 844)
[M::mem_pestat] mean and std.dev: (316.08, 148.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1059)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::process] read 684824 sequences (100000109 bp) in 1.330 CPU sec, 1.335 real sec...
[M::mem_process_seqs] Processed 684826 reads in 135.594 CPU sec, 4.309 real sec
sorting block 19, #reads = 1072194 mem = 536882849 peak = 925073408
[M::mem_process_seqs] Processed 684560 reads in 84.884 CPU sec, 2.687 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (15, 284971, 1, 10)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (260, 260, 260)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (260, 260)
[M::mem_pestat] mean and std.dev: (260.00, 0.00)
[M::mem_pestat] low and high boundaries for proper pairs: (260, 260)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 299, 415)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 843)
[M::mem_pestat] mean and std.dev: (317.43, 148.47)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1057)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (124, 256, 388)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 916)
[M::mem_pestat] mean and std.dev: (283.00, 148.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1180)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
sorting block 20, #reads = 1071522 mem = 536878257 peak = 956260352
[M::process] read 684442 sequences (100000231 bp) in 2.031 CPU sec, 2.177 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 285011, 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, 298, 418)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 858)
[M::mem_pestat] mean and std.dev: (318.29, 151.96)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1078)
[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 683994 reads in 136.378 CPU sec, 4.354 real sec
[M::process] read 683738 sequences (100000098 bp) in 1.430 CPU sec, 1.427 real sec...
[M::mem_process_seqs] Processed 684824 reads in 86.681 CPU sec, 2.748 real sec
sorting block 21, #reads = 1069857 mem = 536877241 peak = 956260352
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 284433, 1, 2)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (120, 237, 717)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1911)
[M::mem_pestat] mean and std.dev: (243.25, 194.05)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2508)
[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: (325.17, 155.19)
[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 685196 sequences (100000084 bp) in 2.315 CPU sec, 2.424 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 284389, 2, 11)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (122, 191, 217)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 407)
[M::mem_pestat] mean and std.dev: (173.60, 45.95)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 502)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 308, 429)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 881)
[M::mem_pestat] mean and std.dev: (325.92, 154.20)
[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: (160, 273, 3861)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11263)
[M::mem_pestat] mean and std.dev: (1553.09, 1788.91)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 14964)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::process] read 684062 sequences (100000096 bp) in 1.330 CPU sec, 1.334 real sec...
[M::mem_process_seqs] Processed 684442 reads in 137.169 CPU sec, 4.364 real sec
[M::mem_process_seqs] Processed 683738 reads in 86.111 CPU sec, 2.727 real sec
sorting block 22, #reads = 1069816 mem = 536880038 peak = 956260352
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 285565, 0, 13)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (197, 296, 413)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 845)
[M::mem_pestat] mean and std.dev: (315.07, 149.18)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1061)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (259, 306, 2107)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5803)
[M::mem_pestat] mean and std.dev: (712.46, 768.88)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 7651)
[M::mem_pestat] skip orientation RR
[M::process] read 683872 sequences (100000187 bp) in 2.043 CPU sec, 2.156 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 284649, 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: (200, 300, 418)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 854)
[M::mem_pestat] mean and std.dev: (318.77, 150.39)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1072)
[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 683856 sequences (100000154 bp) in 1.340 CPU sec, 1.337 real sec...
[M::mem_process_seqs] Processed 685196 reads in 136.497 CPU sec, 4.351 real sec
[M::mem_process_seqs] Processed 684062 reads in 85.088 CPU sec, 2.698 real sec
sorting block 23, #reads = 1069423 mem = 536876832 peak = 956260352
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (20, 284770, 1, 5)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (188, 216, 696)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1712)
[M::mem_pestat] mean and std.dev: (357.20, 279.54)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2220)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 301, 419)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 853)
[M::mem_pestat] mean and std.dev: (320.28, 151.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1070)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
sorting block 24, #reads = 1070610 mem = 536877994 peak = 956260352
[M::process] read 684642 sequences (100000288 bp) in 2.087 CPU sec, 2.205 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 284516, 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: (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: (322.21, 153.60)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1085)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 682466 sequences (100000120 bp) in 1.310 CPU sec, 1.314 real sec...
[M::mem_process_seqs] Processed 683872 reads in 138.005 CPU sec, 4.413 real sec
[M::mem_process_seqs] Processed 683856 reads in 87.460 CPU sec, 2.780 real sec
sorting block 25, #reads = 1070230 mem = 536879564 peak = 956260352
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 284842, 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: (200, 301, 424)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 872)
[M::mem_pestat] mean and std.dev: (321.79, 154.47)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1096)
[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 683222 sequences (100000086 bp) in 2.071 CPU sec, 2.238 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 283987, 4, 12)
[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, 314, 433)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 881)
[M::mem_pestat] mean and std.dev: (329.79, 153.11)
[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] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (214, 216, 226)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (190, 250)
[M::mem_pestat] mean and std.dev: (216.90, 4.78)
[M::mem_pestat] low and high boundaries for proper pairs: (178, 262)
[M::mem_pestat] skip orientation RR
[M::process] read 684230 sequences (100000206 bp) in 1.320 CPU sec, 1.320 real sec...
[M::mem_process_seqs] Processed 684642 reads in 137.960 CPU sec, 4.404 real sec
[M::mem_process_seqs] Processed 682466 reads in 85.153 CPU sec, 2.709 real sec
sorting block 26, #reads = 1069017 mem = 536879895 peak = 956260352
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 284504, 1, 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, 309, 426)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 866)
[M::mem_pestat] mean and std.dev: (325.59, 152.52)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1086)
[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 683464 sequences (100000173 bp) in 2.342 CPU sec, 2.503 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 284534, 2, 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: (200, 299, 414)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 842)
[M::mem_pestat] mean and std.dev: (316.79, 148.65)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1056)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 683252 sequences (100000277 bp) in 1.340 CPU sec, 1.342 real sec...
[M::mem_process_seqs] Processed 683222 reads in 134.159 CPU sec, 4.269 real sec
[M::mem_process_seqs] Processed 684230 reads in 84.493 CPU sec, 2.678 real sec
sorting block 27, #reads = 1069413 mem = 536880065 peak = 956260352
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 284858, 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: (203, 302, 417)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 845)
[M::mem_pestat] mean and std.dev: (319.56, 148.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1059)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::process] read 683814 sequences (100000210 bp) in 2.055 CPU sec, 2.160 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (12, 284563, 2, 3)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (103, 230, 363)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 883)
[M::mem_pestat] mean and std.dev: (189.55, 102.06)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1143)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (203, 302, 420)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 854)
[M::mem_pestat] mean and std.dev: (321.09, 151.14)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1071)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::process] read 685258 sequences (100000071 bp) in 1.344 CPU sec, 1.352 real sec...
[M::mem_process_seqs] Processed 683464 reads in 137.415 CPU sec, 4.387 real sec
sorting block 28, #reads = 1070877 mem = 536878042 peak = 956260352
[M::mem_process_seqs] Processed 683252 reads in 86.975 CPU sec, 2.753 real sec
sorting block 29, #reads = 1069782 mem = 536876210 peak = 991592448
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (13, 284881, 2, 11)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (122, 182, 702)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1862)
[M::mem_pestat] mean and std.dev: (323.23, 284.08)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2442)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 300, 422)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 864)
[M::mem_pestat] mean and std.dev: (321.61, 153.78)
[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: (165, 200, 425)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 945)
[M::mem_pestat] mean and std.dev: (258.18, 121.66)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1205)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::process] read 682906 sequences (100000274 bp) in 2.329 CPU sec, 2.434 real sec...
[M::process] read 684212 sequences (100000234 bp) in 1.340 CPU sec, 1.340 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 285332, 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: (198, 302, 430)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 894)
[M::mem_pestat] mean and std.dev: (324.23, 158.25)
[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] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 683814 reads in 143.645 CPU sec, 4.573 real sec
[M::mem_process_seqs] Processed 685258 reads in 87.971 CPU sec, 2.791 real sec
sorting block 30, #reads = 1068001 mem = 536877689 peak = 991592448
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 284470, 1, 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: (207, 317, 445)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 921)
[M::mem_pestat] mean and std.dev: (335.79, 160.80)
[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::process] read 683556 sequences (100000074 bp) in 2.027 CPU sec, 2.131 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 285436, 0, 2)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (185, 185, 471)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1043)
[M::mem_pestat] mean and std.dev: (350.36, 253.86)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1366)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (202, 305, 429)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 883)
[M::mem_pestat] mean and std.dev: (325.17, 155.52)
[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 683462 sequences (100000301 bp) in 1.340 CPU sec, 1.337 real sec...
[M::mem_process_seqs] Processed 682906 reads in 136.608 CPU sec, 4.355 real sec
[M::mem_process_seqs] Processed 684212 reads in 86.081 CPU sec, 2.733 real sec
sorting block 31, #reads = 1069608 mem = 536879698 peak = 991592448
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 284700, 0, 9)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (119, 128, 192)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 338)
[M::mem_pestat] mean and std.dev: (145.73, 39.38)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 411)
[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: (325.10, 155.16)
[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_pestat] skip orientation FF
[M::process] read 683272 sequences (100000093 bp) in 2.173 CPU sec, 2.302 real sec...
[M::process] read 392718 sequences (57460573 bp) in 0.910 CPU sec, 0.912 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 284512, 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: (201, 300, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 861)
[M::mem_pestat] mean and std.dev: (321.32, 153.85)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1081)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (207, 227, 252)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (117, 342)
[M::mem_pestat] mean and std.dev: (210.38, 38.42)
[M::mem_pestat] low and high boundaries for proper pairs: (57, 387)
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 683556 reads in 137.627 CPU sec, 4.403 real sec
[M::mem_process_seqs] Processed 683462 reads in 86.700 CPU sec, 2.759 real sec
sorting block 32, #reads = 1071285 mem = 536880419 peak = 991592448
sorting block 33, #reads = 1070086 mem = 536880147 peak = 1137295360
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (15, 283739, 4, 5)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (175, 319, 455)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1015)
[M::mem_pestat] mean and std.dev: (269.08, 134.42)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1295)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (201, 300, 419)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 855)
[M::mem_pestat] mean and std.dev: (320.46, 152.33)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1073)
[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): (3, 163670, 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: (202, 301, 420)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 856)
[M::mem_pestat] mean and std.dev: (321.30, 153.28)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1074)
[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 683272 reads in 106.778 CPU sec, 3.483 real sec
[M::mem_process_seqs] Processed 392718 reads in 53.128 CPU sec, 1.723 real sec
sorting block 34, #reads = 1069596 mem = 536880325 peak = 1137295360
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: 37315374
overall: 69763301376 mem 5358.758 user 302.525 sys 733.599 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_0004_B23KGCJLT4_1.L005\tPU:L005\tSM:NA12878_c_0002_gDNA_0004_B23KGCJLT4_1\tLB:NA12878_c_0002_gDNA_0004_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_0004_B23KGCJLT4_1_R1.fastq.gz NA12878_c_0002_gDNA_0004_B23KGCJLT4_1_R2.fastq.gz
[main] Real time: 733.644 sec; CPU: 5661.295 sec
sorting block 35, #reads = 16892 mem = 8485478 peak = 1137295360
uniq header count 1
merging 36 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: 1971996531
output reads: 37493792
bam_mem_sort: 36 calls 14.054 user 0.130 sys 14.268 real
bam_write: 36 calls 20.429 user 0.602 sys 21.193 real
execute: 1 calls 7.443 user 0.491 sys 743.826 real
merge_files: 1 calls 7.433 user 0.463 sys 10.192 real
parse_chunk: 561 calls 17.724 user 5.206 sys 23.275 real
read_chunk: 1515 calls 13.123 user 13.477 sys 130.178 real
sort_block: 1 calls 10.897 user 13.045 sys 126.362 real
write_chunk: 952 calls 7.099 user 0.312 sys 9.517 real
overall: 2352697344 mem 388.450 user 25.628 sys 743.853 real
ls: cannot access '*.cram': No such file or directory