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: 0.391 sec; CPU: 0.016 sec Read 100000 spots for SRR1972920 Written 100000 spots for SRR1972920 Read 100000 spots for SRR1972917 Written 100000 spots for SRR1972917 Read 100000 spots for SRR1972918 Written 100000 spots for SRR1972918 Read 100000 spots for SRR1972921 Written 100000 spots for SRR1972921 Read 100000 spots for SRR1972919 Written 100000 spots for SRR1972919 [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): (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_process_seqs] Processed 99010 reads in 2.384 CPU sec, 2.319 real sec [M::mem_process_seqs] Processed 99010 reads in 2.416 CPU sec, 2.345 real sec [M::mem_process_seqs] Processed 99010 reads in 2.444 CPU sec, 2.370 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): (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_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 4.080 CPU sec, 4.005 real sec [M::mem_process_seqs] Processed 99010 reads in 4.004 CPU sec, 4.015 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): (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_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 2.344 CPU sec, 2.312 real sec [M::mem_process_seqs] Processed 99010 reads in 2.384 CPU sec, 2.356 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): (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 0.080 CPU sec, 0.067 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 0.088 CPU sec, 0.070 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: 4.826 sec; CPU: 4.924 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: 4.828 sec; CPU: 4.924 sec [M::mem_process_seqs] Processed 99010 reads in 2.464 CPU sec, 2.440 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 0.088 CPU sec, 0.076 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: 4.970 sec; CPU: 5.068 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): (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 2.596 CPU sec, 2.568 real sec [M::mem_process_seqs] Processed 99010 reads in 2.684 CPU sec, 2.649 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 0.104 CPU sec, 0.078 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, 0.043 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: 6.745 sec; CPU: 6.784 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: 6.766 sec; CPU: 6.880 sec [mpileup] 5 samples in 5 input files