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: 0.357 sec; CPU: 0.016 sec
Read 100000 spots for SRR1972919
Written 100000 spots for SRR1972919
Read 100000 spots for SRR1972917
Written 100000 spots for SRR1972917
Read 100000 spots for SRR1972920
Written 100000 spots for SRR1972920
Read 100000 spots for SRR1972921
Written 100000 spots for SRR1972921
Read 100000 spots for SRR1972918
Written 100000 spots for SRR1972918
[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): (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): (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): (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 2.412 CPU sec, 2.355 real sec
[M::mem_process_seqs] Processed 99010 reads in 2.424 CPU sec, 2.366 real sec
[M::mem_process_seqs] Processed 99010 reads in 2.456 CPU sec, 2.389 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): (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): (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 3.944 CPU sec, 3.877 real sec
[M::process] read 1980 sequences (199980 bp)...
[M::mem_process_seqs] Processed 99010 reads in 4.092 CPU sec, 4.026 real sec
[M::process] read 1980 sequences (199980 bp)...
[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 2.384 CPU sec, 2.364 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 0.104 CPU sec, 0.076 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/KJ660346.fa reads/SRR1972917_1.fastq reads/SRR1972917_2.fastq
[main] Real time: 4.890 sec; CPU: 4.988 sec
[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
[M::mem_process_seqs] Processed 99010 reads in 2.688 CPU sec, 2.661 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 0.092 CPU sec, 0.075 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: 5.190 sec; CPU: 5.276 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_process_seqs] Processed 99010 reads in 2.992 CPU sec, 2.970 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 0.104 CPU sec, 0.080 real 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: 5.508 sec; CPU: 5.608 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)
[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 2.448 CPU sec, 2.412 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 0.072 CPU sec, 0.049 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/KJ660346.fa reads/SRR1972920_1.fastq reads/SRR1972920_2.fastq
[main] Real time: 6.420 sec; CPU: 6.544 sec
[M::mem_process_seqs] Processed 99010 reads in 2.420 CPU sec, 2.383 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 0.060 CPU sec, 0.041 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: 6.555 sec; CPU: 6.660 sec
[mpileup] 5 samples in 5 input files