[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/AF086833.fa
[main] Real time: 0.393 sec; CPU: 0.016 sec
Read 100000 spots for SRR1553500
Written 100000 spots for SRR1553500
[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::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3998, 39956, 185, 3805)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (95, 165, 267)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 611)
[M::mem_pestat] mean and std.dev: (190.39, 125.74)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 783)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (151, 250, 387)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 859)
[M::mem_pestat] mean and std.dev: (282.58, 168.15)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1095)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (42, 120, 253)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 675)
[M::mem_pestat] mean and std.dev: (147.49, 132.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 886)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (96, 173, 287)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 669)
[M::mem_pestat] mean and std.dev: (201.57, 134.91)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 860)
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 99010 reads in 7.020 CPU sec, 6.969 real sec
[M::process] read 1980 sequences (199980 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4068, 39458, 189, 4091)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (95, 167, 278)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 644)
[M::mem_pestat] mean and std.dev: (194.10, 130.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 827)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (146, 246, 384)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 860)
[M::mem_pestat] mean and std.dev: (278.87, 168.57)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1098)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (41, 113, 245)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 653)
[M::mem_pestat] mean and std.dev: (139.64, 127.62)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 857)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (98, 171, 278)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 638)
[M::mem_pestat] mean and std.dev: (197.06, 129.78)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 818)
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 99010 reads in 6.356 CPU sec, 6.312 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (84, 795, 5, 84)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (100, 146, 254)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 562)
[M::mem_pestat] mean and std.dev: (192.30, 131.35)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 718)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (142, 244, 387)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 877)
[M::mem_pestat] mean and std.dev: (282.35, 177.10)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1122)
[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: (88, 204, 345)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 859)
[M::mem_pestat] mean and std.dev: (215.46, 140.36)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1116)
[M::mem_process_seqs] Processed 1980 reads in 0.172 CPU sec, 0.144 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -R @RG\tID:SRR1553500\tSM:SRR1553500\tLB:SRR1553500 refs/AF086833.fa SRR1553500_1.fastq SRR1553500_2.fastq
[main] Real time: 13.511 sec; CPU: 13.604 sec
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid