[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 3601228 sequences (400000229 bp)...
[M::process] read 3598282 sequences (400000025 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 851337, 9, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (88, 113, 143)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 253)
[M::mem_pestat] mean and std.dev: (116.85, 40.91)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 308)
[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 3601228 reads in 5873.497 CPU sec, 147.321 real sec
[M::process] read 3598550 sequences (400000026 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 852546, 11, 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: (88, 113, 143)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 253)
[M::mem_pestat] mean and std.dev: (116.91, 40.86)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 308)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (175, 5493, 5493)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16129)
[M::mem_pestat] mean and std.dev: (3306.18, 2931.86)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 21447)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 3598282 reads in 5994.154 CPU sec, 150.528 real sec
[M::process] read 3594220 sequences (400000033 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 851763, 11, 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: (88, 113, 143)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 253)
[M::mem_pestat] mean and std.dev: (116.92, 40.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 308)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (131, 353, 1552)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4394)
[M::mem_pestat] mean and std.dev: (716.27, 835.36)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 5815)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 3598550 reads in 6002.065 CPU sec, 151.127 real sec
[M::process] read 3604738 sequences (400000176 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 851371, 4, 3)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (88, 113, 143)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 253)
[M::mem_pestat] mean and std.dev: (117.08, 41.06)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 308)
[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 3594220 reads in 6016.075 CPU sec, 150.728 real sec
[M::process] read 3605830 sequences (400000095 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 845791, 12, 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: (88, 114, 144)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 256)
[M::mem_pestat] mean and std.dev: (117.70, 41.44)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 312)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (82, 223, 267)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 637)
[M::mem_pestat] mean and std.dev: (161.27, 106.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 822)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 3604738 reads in 6001.990 CPU sec, 151.095 real sec
[M::process] read 3602262 sequences (400000158 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 847918, 14, 2)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (88, 114, 144)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 256)
[M::mem_pestat] mean and std.dev: (117.74, 41.40)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 312)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (25, 397, 5677)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16981)
[M::mem_pestat] mean and std.dev: (1992.00, 2977.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 22633)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 3605830 reads in 6071.868 CPU sec, 152.075 real sec
[M::process] read 3590038 sequences (400000101 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 845844, 9, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (88, 114, 144)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 256)
[M::mem_pestat] mean and std.dev: (117.85, 41.51)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 312)
[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 3602262 reads in 6188.101 CPU sec, 155.693 real sec
[M::process] read 3586700 sequences (400000205 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 846460, 8, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (88, 113, 144)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 256)
[M::mem_pestat] mean and std.dev: (117.52, 41.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 312)
[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 3590038 reads in 6062.942 CPU sec, 151.820 real sec
[M::process] read 3593956 sequences (400000177 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 846797, 11, 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: (88, 113, 144)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 256)
[M::mem_pestat] mean and std.dev: (117.48, 41.42)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 312)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (325, 555, 1328)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3334)
[M::mem_pestat] mean and std.dev: (713.00, 781.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4337)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 3586700 reads in 6057.062 CPU sec, 152.210 real sec
[M::process] read 3589468 sequences (400000107 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 848836, 11, 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: (88, 113, 143)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 253)
[M::mem_pestat] mean and std.dev: (117.03, 40.91)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 308)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (108, 160, 3226)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9462)
[M::mem_pestat] mean and std.dev: (1670.09, 2393.47)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 12580)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 3593956 reads in 6066.275 CPU sec, 152.714 real sec
[M::process] read 3585566 sequences (400000033 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 848442, 15, 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: (88, 113, 143)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 253)
[M::mem_pestat] mean and std.dev: (117.13, 41.04)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 308)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (121, 267, 591)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1531)
[M::mem_pestat] mean and std.dev: (357.86, 344.18)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2001)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 3589468 reads in 6031.103 CPU sec, 151.397 real sec
[M::process] read 3596388 sequences (400000005 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 842117, 10, 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: (88, 114, 145)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 259)
[M::mem_pestat] mean and std.dev: (118.15, 41.94)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 316)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (25, 6269, 7740)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 23170)
[M::mem_pestat] mean and std.dev: (4364.40, 3548.72)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 30885)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 3585566 reads in 6083.108 CPU sec, 152.855 real sec
[M::process] read 3596630 sequences (400000052 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 842884, 9, 2)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (88, 114, 144)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 256)
[M::mem_pestat] mean and std.dev: (117.96, 41.66)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 312)
[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 3596388 reads in 6277.429 CPU sec, 157.704 real sec
[M::process] read 3593834 sequences (400000223 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 843912, 12, 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: (88, 114, 144)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 256)
[M::mem_pestat] mean and std.dev: (117.91, 41.52)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 312)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (49, 189, 6977)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 20833)
[M::mem_pestat] mean and std.dev: (2158.33, 3376.25)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 27761)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 3596630 reads in 6843.320 CPU sec, 171.350 real sec
[M::process] read 3579058 sequences (400000205 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 845356, 14, 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: (88, 114, 144)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 256)
[M::mem_pestat] mean and std.dev: (117.82, 41.51)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 312)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (72, 224, 2689)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7923)
[M::mem_pestat] mean and std.dev: (1518.14, 1813.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 10540)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 3593834 reads in 6164.361 CPU sec, 155.211 real sec
[M::process] read 3565272 sequences (400000002 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 846723, 15, 2)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (88, 113, 143)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 253)
[M::mem_pestat] mean and std.dev: (117.33, 40.91)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 308)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (373, 430, 1506)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3772)
[M::mem_pestat] mean and std.dev: (583.31, 510.57)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 4905)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 3579058 reads in 6514.493 CPU sec, 172.372 real sec
[M::process] read 3572734 sequences (400000169 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 843793, 4, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (88, 113, 144)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 256)
[M::mem_pestat] mean and std.dev: (117.71, 41.14)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 312)
[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 3565272 reads in 6097.719 CPU sec, 153.111 real sec
[M::process] read 3577386 sequences (400000006 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 842969, 11, 2)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (88, 113, 144)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 256)
[M::mem_pestat] mean and std.dev: (117.72, 41.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 312)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (715, 1495, 2277)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5401)
[M::mem_pestat] mean and std.dev: (1330.80, 858.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 6963)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 3572734 reads in 6232.667 CPU sec, 156.455 real sec
[M::process] read 3317346 sequences (372066675 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 841461, 16, 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: (89, 114, 144)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 254)
[M::mem_pestat] mean and std.dev: (117.78, 41.06)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 309)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (279, 1195, 3054)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8604)
[M::mem_pestat] mean and std.dev: (1122.00, 1109.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 11379)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 3577386 reads in 6321.327 CPU sec, 159.231 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 782432, 7, 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: (89, 114, 144)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 254)
[M::mem_pestat] mean and std.dev: (117.94, 41.20)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 309)
[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 3317346 reads in 5806.192 CPU sec, 146.508 real sec
[main] Version: 0.7.17-r1188
[main] CMD: /home/shared/bwa-0.7.17/bwa mem -M -t 40 ../data/bwa-GCF_031168955.1_ASM3116895v1_genomic ../data/trimmed-fastqs-heatwave-genetics/MHW198_trimmed_clipped_R1_paired.fq.gz ../data/trimmed-fastqs-heatwave-genetics/MHW198_trimmed_clipped_R2_paired.fq.gz
[main] Real time: 3104.771 sec; CPU: 122717.707 sec