[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.01 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index refs/AF086833.fa
[main] Real time: 0.324 sec; CPU: 0.008 sec
Read 100000 spots for SRR1972919
Written 100000 spots for SRR1972919
Read 100000 spots for SRR1972921
Written 100000 spots for SRR1972921
Read 100000 spots for SRR1972917
Written 100000 spots for SRR1972917
Read 100000 spots for SRR1972918
Written 100000 spots for SRR1972918
Read 100000 spots for SRR1972920
Written 100000 spots for SRR1972920
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 99010 sequences (10000010 bp)...
[M::process] read 99010 sequences (10000010 bp)...
[M::process] read 99010 sequences (10000010 bp)...
[M::process] read 99010 sequences (10000010 bp)...
[M::process] read 99010 sequences (10000010 bp)...
[M::process] read 99010 sequences (10000010 bp)...
[M::process] read 99010 sequences (10000010 bp)...
[M::process] read 99010 sequences (10000010 bp)...
[M::process] read 99010 sequences (10000010 bp)...
[M::process] read 99010 sequences (10000010 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (60, 710, 0, 50)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (43, 71, 132)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 310)
[M::mem_pestat] mean and std.dev: (89.71, 61.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 399)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (72, 97, 133)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 255)
[M::mem_pestat] mean and std.dev: (108.12, 46.44)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 316)
[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: (40, 85, 126)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 298)
[M::mem_pestat] mean and std.dev: (89.43, 54.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 384)
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (183, 1855, 0, 217)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (50, 78, 117)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 251)
[M::mem_pestat] mean and std.dev: (86.89, 45.30)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 318)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (83, 116, 156)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 302)
[M::mem_pestat] mean and std.dev: (124.95, 53.39)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 375)
[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: (47, 80, 113)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 245)
[M::mem_pestat] mean and std.dev: (83.70, 46.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 311)
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 29, 0, 2)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (68, 105, 118)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 218)
[M::mem_pestat] mean and std.dev: (99.45, 40.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 268)
[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 99010 reads in 2.404 CPU sec, 2.338 real sec
[M::mem_process_seqs] Processed 99010 reads in 2.400 CPU sec, 2.337 real sec
[M::mem_process_seqs] Processed 99010 reads in 2.540 CPU sec, 2.485 real sec
[M::process] read 1980 sequences (199980 bp)...
[M::process] read 1980 sequences (199980 bp)...
[M::process] read 1980 sequences (199980 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (12, 106, 0, 11)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (70, 86, 101)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (8, 163)
[M::mem_pestat] mean and std.dev: (84.00, 36.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 231)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (100, 138, 181)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 343)
[M::mem_pestat] mean and std.dev: (142.79, 59.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 424)
[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: (76, 97, 174)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 370)
[M::mem_pestat] mean and std.dev: (116.82, 63.10)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 60, 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: (98, 203, 244)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 536)
[M::mem_pestat] mean and std.dev: (185.48, 97.06)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 682)
[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 99010 reads in 3.820 CPU sec, 3.804 real sec
[M::mem_process_seqs] Processed 99010 reads in 3.836 CPU sec, 3.817 real sec
[M::process] read 1980 sequences (199980 bp)...
[M::process] read 1980 sequences (199980 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (130, 2163, 2, 223)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (68, 106, 141)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 287)
[M::mem_pestat] mean and std.dev: (110.41, 57.86)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 360)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (97, 134, 183)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 355)
[M::mem_pestat] mean and std.dev: (142.02, 60.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 441)
[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: (52, 82, 126)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 274)
[M::mem_pestat] mean and std.dev: (92.12, 53.12)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 348)
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 45, 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: (86, 106, 133)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 227)
[M::mem_pestat] mean and std.dev: (110.82, 32.78)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 274)
[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 99010 reads in 2.540 CPU sec, 2.507 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 1, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[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 1980 reads in 0.088 CPU sec, 0.079 real sec
[M::mem_process_seqs] Processed 99010 reads in 2.560 CPU sec, 2.529 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/AF086833.fa reads/SRR1972919_1.fastq reads/SRR1972919_2.fastq
[main] Real time: 5.097 sec; CPU: 5.124 sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 30, 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: (68, 122, 173)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 383)
[M::mem_pestat] mean and std.dev: (129.40, 65.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 488)
[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 1980 reads in 0.052 CPU sec, 0.044 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/AF086833.fa reads/SRR1972918_1.fastq reads/SRR1972918_2.fastq
[main] Real time: 5.240 sec; CPU: 5.220 sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (81, 886, 0, 90)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (53, 75, 120)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 254)
[M::mem_pestat] mean and std.dev: (88.34, 50.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 321)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (97, 138, 187)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 367)
[M::mem_pestat] mean and std.dev: (147.23, 63.76)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 457)
[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: (45, 77, 128)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 294)
[M::mem_pestat] mean and std.dev: (88.77, 53.18)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 377)
[M::mem_process_seqs] Processed 99010 reads in 3.168 CPU sec, 3.157 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 20, 0, 2)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (87, 126, 165)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 321)
[M::mem_pestat] mean and std.dev: (130.10, 64.76)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 399)
[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 1980 reads in 0.072 CPU sec, 0.066 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/AF086833.fa reads/SRR1972921_1.fastq reads/SRR1972921_2.fastq
[main] Real time: 5.731 sec; CPU: 5.740 sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 107, 0, 8)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (68, 93, 122)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 230)
[M::mem_pestat] mean and std.dev: (98.20, 52.09)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 307)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (101, 133, 182)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 344)
[M::mem_pestat] mean and std.dev: (143.98, 61.38)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 425)
[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 99010 reads in 2.412 CPU sec, 2.379 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 2, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[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 1980 reads in 0.056 CPU sec, 0.046 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/AF086833.fa reads/SRR1972917_1.fastq reads/SRR1972917_2.fastq
[main] Real time: 6.411 sec; CPU: 6.396 sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 33, 2, 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: (153, 178, 273)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 513)
[M::mem_pestat] mean and std.dev: (197.59, 80.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 633)
[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 99010 reads in 3.000 CPU sec, 2.974 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 2, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[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 1980 reads in 0.056 CPU sec, 0.046 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/AF086833.fa reads/SRR1972920_1.fastq reads/SRR1972920_2.fastq
[main] Real time: 6.986 sec; CPU: 6.972 sec
[mpileup] 5 samples in 5 input files