Readseq version 2.1.30 (12-May-2010)
Readseq version 2.1.30 (12-May-2010)
[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... 0.01 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index refs/KJ660346.fa
[main] Real time: 0.306 sec; CPU: 0.020 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): (4, 70, 0, 9)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (110, 204, 245)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 515)
[M::mem_pestat] mean and std.dev: (193.86, 96.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 650)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (65, 745, 0, 54)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (43, 69, 132)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 310)
[M::mem_pestat] mean and std.dev: (89.61, 58.87)
[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: (73, 98, 133)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 253)
[M::mem_pestat] mean and std.dev: (107.44, 44.98)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 313)
[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: (49, 90, 128)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 286)
[M::mem_pestat] mean and std.dev: (93.53, 54.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 365)
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 36, 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: (79, 109, 135)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 247)
[M::mem_pestat] mean and std.dev: (108.25, 44.10)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 303)
[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 2.352 CPU sec, 2.280 real sec
[M::mem_process_seqs] Processed 99010 reads in 2.364 CPU sec, 2.293 real sec
[M::mem_process_seqs] Processed 99010 reads in 2.388 CPU sec, 2.334 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): (16, 108, 0, 12)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (40, 86, 101)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 223)
[M::mem_pestat] mean and std.dev: (78.50, 43.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 284)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (95, 135, 181)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 353)
[M::mem_pestat] mean and std.dev: (140.24, 60.15)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 439)
[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, 119, 179)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 385)
[M::mem_pestat] mean and std.dev: (122.00, 62.81)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 488)
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (204, 2007, 1, 227)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (49, 78, 115)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 247)
[M::mem_pestat] mean and std.dev: (85.33, 44.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 313)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (84, 118, 159)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 309)
[M::mem_pestat] mean and std.dev: (126.28, 53.69)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 384)
[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: (44, 80, 114)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 254)
[M::mem_pestat] mean and std.dev: (86.41, 50.90)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 324)
[M::mem_process_seqs] Processed 99010 reads in 3.880 CPU sec, 3.811 real sec
[M::process] read 1980 sequences (199980 bp)...
[M::mem_process_seqs] Processed 99010 reads in 4.032 CPU sec, 4.010 real sec
[M::process] read 1980 sequences (199980 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 39, 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: (152, 177, 254)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 458)
[M::mem_pestat] mean and std.dev: (183.16, 64.30)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 560)
[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 2.364 CPU sec, 2.335 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 0.084 CPU sec, 0.079 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (98, 985, 0, 104)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (53, 77, 119)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 251)
[M::mem_pestat] mean and std.dev: (89.93, 50.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 317)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (98, 140, 191)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 377)
[M::mem_pestat] mean and std.dev: (148.62, 64.39)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 470)
[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, 80, 128)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 294)
[M::mem_pestat] mean and std.dev: (91.08, 54.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 377)
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 53, 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: (87, 107, 138)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 240)
[M::mem_pestat] mean and std.dev: (114.13, 34.84)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 291)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/KJ660346.fa reads/SRR1972920_1.fastq reads/SRR1972920_2.fastq
[main] Real time: 4.823 sec; CPU: 4.864 sec
[M::mem_process_seqs] Processed 99010 reads in 2.476 CPU sec, 2.458 real sec
[M::mem_process_seqs] Processed 99010 reads in 2.496 CPU sec, 2.473 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, 0.078 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 21, 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: (80, 115, 165)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 335)
[M::mem_pestat] mean and std.dev: (126.86, 65.08)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 420)
[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 0.084 CPU sec, 0.077 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/KJ660346.fa reads/SRR1972919_1.fastq reads/SRR1972919_2.fastq
[main] Real time: 4.990 sec; CPU: 5.016 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/KJ660346.fa reads/SRR1972921_1.fastq reads/SRR1972921_2.fastq
[main] Real time: 5.027 sec; CPU: 5.036 sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 118, 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: (98, 144, 186)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 362)
[M::mem_pestat] mean and std.dev: (147.26, 63.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 450)
[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 2.872 CPU sec, 2.840 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
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (173, 2555, 3, 263)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (57, 94, 138)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 300)
[M::mem_pestat] mean and std.dev: (101.92, 58.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 381)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (99, 136, 185)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 357)
[M::mem_pestat] mean and std.dev: (143.75, 60.09)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 443)
[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: (51, 81, 122)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 264)
[M::mem_pestat] mean and std.dev: (90.60, 52.52)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 335)
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/KJ660346.fa reads/SRR1972917_1.fastq reads/SRR1972917_2.fastq
[main] Real time: 6.840 sec; CPU: 6.868 sec
[M::mem_process_seqs] Processed 99010 reads in 2.900 CPU sec, 2.866 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 41, 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: (94, 129, 176)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 340)
[M::mem_pestat] mean and std.dev: (136.32, 59.73)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 422)
[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 0.048 CPU sec, 0.040 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/KJ660346.fa reads/SRR1972918_1.fastq reads/SRR1972918_2.fastq
[main] Real time: 7.100 sec; CPU: 7.076 sec
[mpileup] 5 samples in 5 input files