基因数据处理56之bwa运行paird-end（1千万条100bp的reads）.md

（1）pair1.fq》sai

    bwa aln GRCH38BWAindex/GRCH38chr1L3556522.fasta g38L100c10000000Nhs20Paired1.fq >g38L100c10000000Nhs20Paired1.sai

pair1记录：

    hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ bwa aln GRCH38BWAindex/GRCH38chr1L3556522.fasta g38L100c10000000Nhs20Paired1.fq >g38L100c10000000Nhs20Paired1.sai    [bwa_aln] 17bp reads: max_diff = 2    [bwa_aln] 38bp reads: max_diff = 3    [bwa_aln] 64bp reads: max_diff = 4    [bwa_aln] 93bp reads: max_diff = 5    [bwa_aln] 124bp reads: max_diff = 6    [bwa_aln] 157bp reads: max_diff = 7    [bwa_aln] 190bp reads: max_diff = 8    [bwa_aln] 225bp reads: max_diff = 9    [bwa_aln_core] calculate SA coordinate... 40.82 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 262144 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 41.14 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 524288 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.22 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 786432 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.27 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 1048576 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 40.83 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 1310720 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 40.88 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 1572864 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.32 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 1835008 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.39 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 2097152 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 40.87 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 2359296 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.12 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 2621440 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 40.95 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 2883584 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.28 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 3145728 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.28 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 3407872 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.13 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 3670016 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.00 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 3932160 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.15 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 4194304 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 41.36 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 4456448 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 40.90 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 4718592 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 41.05 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 4980736 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 41.08 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 5242880 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 42.93 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 5505024 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.28 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 5767168 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.39 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 6029312 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 41.11 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 6291456 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 40.47 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 6553600 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 40.78 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 6815744 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 40.86 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 7077888 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 40.95 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 7340032 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 41.03 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 7602176 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 40.81 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 7864320 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.02 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 8126464 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 40.78 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 8388608 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 40.83 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 8650752 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.32 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 8912896 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 43.34 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 9175040 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 12.48 sec    [bwa_aln_core] write to the disk... 0.01 sec    [bwa_aln_core] 9256331 sequences have been processed.    [main] Version: 0.7.13-r1126    [main] CMD: bwa aln GRCH38BWAindex/GRCH38chr1L3556522.fasta g38L100c10000000Nhs20Paired1.fq    [main] Real time: 1518.448 sec; CPU: 1496.862 sec

(2)pair2.fq>sai

    hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ bwa aln GRCH38BWAindex/GRCH38chr1L3556522.fasta g38L100c10000000Nhs20Paired2.fq >g38L100c10000000Nhs20Paired2.sai    [bwa_aln] 17bp reads: max_diff = 2    [bwa_aln] 38bp reads: max_diff = 3    [bwa_aln] 64bp reads: max_diff = 4    [bwa_aln] 93bp reads: max_diff = 5    [bwa_aln] 124bp reads: max_diff = 6    [bwa_aln] 157bp reads: max_diff = 7    [bwa_aln] 190bp reads: max_diff = 8    [bwa_aln] 225bp reads: max_diff = 9    [bwa_aln_core] calculate SA coordinate... 53.65 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 262144 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 54.61 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 524288 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 56.88 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 786432 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 57.31 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 1048576 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 56.92 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 1310720 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 57.49 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 1572864 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 57.12 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 1835008 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 57.36 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 2097152 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 54.36 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 2359296 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 57.00 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 2621440 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 56.90 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 2883584 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 57.42 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 3145728 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 56.77 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 3407872 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 54.13 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 3670016 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 57.01 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 3932160 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 56.99 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 4194304 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 54.55 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 4456448 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 54.29 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 4718592 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 57.02 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 4980736 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 54.09 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 5242880 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 56.99 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 5505024 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 54.41 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 5767168 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 53.68 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 6029312 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 56.68 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 6291456 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 57.49 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 6553600 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 54.37 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 6815744 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 57.05 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 7077888 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 57.08 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 7340032 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 54.23 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 7602176 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 53.93 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 7864320 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 54.36 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 8126464 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 53.86 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 8388608 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 53.96 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 8650752 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 54.55 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 8912896 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 54.07 sec    [bwa_aln_core] write to the disk... 0.03 sec    [bwa_aln_core] 9175040 sequences have been processed.    [bwa_aln_core] calculate SA coordinate... 16.78 sec    [bwa_aln_core] write to the disk... 0.01 sec    [bwa_aln_core] 9256331 sequences have been processed.    [main] Version: 0.7.13-r1126    [main] CMD: bwa aln GRCH38BWAindex/GRCH38chr1L3556522.fasta g38L100c10000000Nhs20Paired2.fq    [main] Real time: 2003.658 sec; CPU: 1980.403 sec

(3) 匹配：

    hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ bwa sampe GRCH38BWAindex/GRCH38chr1L3556522.fasta g38L100c10000000Nhs20Paired1.sai g38L100c10000000Nhs20Paired2.sai g38L100c10000000Nhs20Paired1.fq g38L100c10000000Nhs20Paired2.fq > g38L100c10000000Nhs20Paired12.bwa.sam    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 244114 pairs: 199.440 +/- 9.960    [infer_isize] skewness: -0.004; kurtosis: -0.071; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.95 sec    [bwa_sai2sam_pe_core] changing coordinates of 5419 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 842 out of 842 Q17 singletons are mated.    [bwa_paired_sw] 13 out of 13 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.18 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.46 sec    [bwa_sai2sam_pe_core] print alignments... 1.88 sec    [bwa_sai2sam_pe_core] 262144 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243856 pairs: 199.509 +/- 9.944    [infer_isize] skewness: -0.008; kurtosis: -0.092; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 8.28 sec    [bwa_sai2sam_pe_core] changing coordinates of 5442 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 853 out of 853 Q17 singletons are mated.    [bwa_paired_sw] 13 out of 16 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.27 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.46 sec    [bwa_sai2sam_pe_core] print alignments... 1.90 sec    [bwa_sai2sam_pe_core] 524288 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243858 pairs: 199.511 +/- 9.954    [infer_isize] skewness: -0.004; kurtosis: -0.087; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 8.26 sec    [bwa_sai2sam_pe_core] changing coordinates of 5510 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 878 out of 878 Q17 singletons are mated.    [bwa_paired_sw] 18 out of 19 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.16 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.46 sec    [bwa_sai2sam_pe_core] print alignments... 1.90 sec    [bwa_sai2sam_pe_core] 786432 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 244096 pairs: 199.499 +/- 9.947    [infer_isize] skewness: 0.006; kurtosis: -0.096; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.49 sec    [bwa_sai2sam_pe_core] changing coordinates of 5362 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 843 out of 843 Q17 singletons are mated.    [bwa_paired_sw] 13 out of 15 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.13 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.92 sec    [bwa_sai2sam_pe_core] 1048576 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 244039 pairs: 199.531 +/- 9.924    [infer_isize] skewness: 0.004; kurtosis: -0.090; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 8.21 sec    [bwa_sai2sam_pe_core] changing coordinates of 5477 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 768 out of 768 Q17 singletons are mated.    [bwa_paired_sw] 19 out of 20 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.15 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.46 sec    [bwa_sai2sam_pe_core] print alignments... 1.92 sec    [bwa_sai2sam_pe_core] 1310720 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243833 pairs: 199.476 +/- 9.941    [infer_isize] skewness: 0.002; kurtosis: -0.091; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 8.00 sec    [bwa_sai2sam_pe_core] changing coordinates of 5493 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 834 out of 834 Q17 singletons are mated.    [bwa_paired_sw] 12 out of 13 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.13 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.46 sec    [bwa_sai2sam_pe_core] print alignments... 1.90 sec    [bwa_sai2sam_pe_core] 1572864 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 244057 pairs: 199.503 +/- 9.933    [infer_isize] skewness: -0.001; kurtosis: -0.096; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.78 sec    [bwa_sai2sam_pe_core] changing coordinates of 5364 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 866 out of 866 Q17 singletons are mated.    [bwa_paired_sw] 9 out of 10 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.15 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.46 sec    [bwa_sai2sam_pe_core] print alignments... 1.91 sec    [bwa_sai2sam_pe_core] 1835008 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 244027 pairs: 199.481 +/- 9.980    [infer_isize] skewness: -0.000; kurtosis: -0.109; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.54 sec    [bwa_sai2sam_pe_core] changing coordinates of 5430 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 804 out of 804 Q17 singletons are mated.    [bwa_paired_sw] 9 out of 11 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.23 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.43 sec    [bwa_sai2sam_pe_core] print alignments... 1.83 sec    [bwa_sai2sam_pe_core] 2097152 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243971 pairs: 199.475 +/- 9.957    [infer_isize] skewness: 0.002; kurtosis: -0.085; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 8.24 sec    [bwa_sai2sam_pe_core] changing coordinates of 5412 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 833 out of 833 Q17 singletons are mated.    [bwa_paired_sw] 15 out of 15 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.18 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.91 sec    [bwa_sai2sam_pe_core] 2359296 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 244088 pairs: 199.514 +/- 9.948    [infer_isize] skewness: 0.003; kurtosis: -0.093; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.45 sec    [bwa_sai2sam_pe_core] changing coordinates of 5521 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 853 out of 853 Q17 singletons are mated.    [bwa_paired_sw] 7 out of 9 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.13 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.43 sec    [bwa_sai2sam_pe_core] print alignments... 1.81 sec    [bwa_sai2sam_pe_core] 2621440 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 244054 pairs: 199.492 +/- 9.961    [infer_isize] skewness: 0.001; kurtosis: -0.080; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.70 sec    [bwa_sai2sam_pe_core] changing coordinates of 5386 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 825 out of 825 Q17 singletons are mated.    [bwa_paired_sw] 10 out of 10 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.23 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.89 sec    [bwa_sai2sam_pe_core] 2883584 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243926 pairs: 199.507 +/- 9.951    [infer_isize] skewness: 0.002; kurtosis: -0.093; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.60 sec    [bwa_sai2sam_pe_core] changing coordinates of 5473 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 831 out of 831 Q17 singletons are mated.    [bwa_paired_sw] 15 out of 15 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.12 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.91 sec    [bwa_sai2sam_pe_core] 3145728 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243802 pairs: 199.476 +/- 9.958    [infer_isize] skewness: 0.006; kurtosis: -0.089; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.54 sec    [bwa_sai2sam_pe_core] changing coordinates of 5572 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 817 out of 817 Q17 singletons are mated.    [bwa_paired_sw] 17 out of 18 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.13 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.43 sec    [bwa_sai2sam_pe_core] print alignments... 1.83 sec    [bwa_sai2sam_pe_core] 3407872 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243845 pairs: 199.518 +/- 9.945    [infer_isize] skewness: 0.000; kurtosis: -0.083; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.26 sec    [bwa_sai2sam_pe_core] changing coordinates of 5518 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 851 out of 851 Q17 singletons are mated.    [bwa_paired_sw] 8 out of 9 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.12 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.92 sec    [bwa_sai2sam_pe_core] 3670016 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243929 pairs: 199.488 +/- 9.950    [infer_isize] skewness: -0.006; kurtosis: -0.094; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.69 sec    [bwa_sai2sam_pe_core] changing coordinates of 5433 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 872 out of 872 Q17 singletons are mated.    [bwa_paired_sw] 10 out of 10 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.12 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.43 sec    [bwa_sai2sam_pe_core] print alignments... 1.82 sec    [bwa_sai2sam_pe_core] 3932160 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 244036 pairs: 199.483 +/- 9.938    [infer_isize] skewness: -0.000; kurtosis: -0.097; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.29 sec    [bwa_sai2sam_pe_core] changing coordinates of 5428 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 807 out of 807 Q17 singletons are mated.    [bwa_paired_sw] 10 out of 11 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.12 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.42 sec    [bwa_sai2sam_pe_core] print alignments... 1.86 sec    [bwa_sai2sam_pe_core] 4194304 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243878 pairs: 199.466 +/- 9.940    [infer_isize] skewness: -0.003; kurtosis: -0.092; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.54 sec    [bwa_sai2sam_pe_core] changing coordinates of 5586 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 858 out of 858 Q17 singletons are mated.    [bwa_paired_sw] 11 out of 11 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.22 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.90 sec    [bwa_sai2sam_pe_core] 4456448 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243722 pairs: 199.534 +/- 9.949    [infer_isize] skewness: 0.001; kurtosis: -0.081; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.68 sec    [bwa_sai2sam_pe_core] changing coordinates of 5512 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 856 out of 856 Q17 singletons are mated.    [bwa_paired_sw] 13 out of 15 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.12 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.43 sec    [bwa_sai2sam_pe_core] print alignments... 1.81 sec    [bwa_sai2sam_pe_core] 4718592 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 244102 pairs: 199.510 +/- 9.928    [infer_isize] skewness: 0.007; kurtosis: -0.081; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.57 sec    [bwa_sai2sam_pe_core] changing coordinates of 5313 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 819 out of 819 Q17 singletons are mated.    [bwa_paired_sw] 14 out of 14 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.17 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.43 sec    [bwa_sai2sam_pe_core] print alignments... 1.80 sec    [bwa_sai2sam_pe_core] 4980736 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243994 pairs: 199.463 +/- 9.955    [infer_isize] skewness: 0.001; kurtosis: -0.104; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.40 sec    [bwa_sai2sam_pe_core] changing coordinates of 5420 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 861 out of 861 Q17 singletons are mated.    [bwa_paired_sw] 16 out of 16 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.12 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.44 sec    [bwa_sai2sam_pe_core] print alignments... 1.91 sec    [bwa_sai2sam_pe_core] 5242880 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243996 pairs: 199.498 +/- 9.936    [infer_isize] skewness: -0.004; kurtosis: -0.083; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.99 sec    [bwa_sai2sam_pe_core] changing coordinates of 5377 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 842 out of 842 Q17 singletons are mated.    [bwa_paired_sw] 8 out of 12 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.15 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.42 sec    [bwa_sai2sam_pe_core] print alignments... 1.81 sec    [bwa_sai2sam_pe_core] 5505024 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243784 pairs: 199.485 +/- 9.950    [infer_isize] skewness: 0.003; kurtosis: -0.095; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.40 sec    [bwa_sai2sam_pe_core] changing coordinates of 5417 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 890 out of 890 Q17 singletons are mated.    [bwa_paired_sw] 13 out of 13 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.13 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.91 sec    [bwa_sai2sam_pe_core] 5767168 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 244130 pairs: 199.473 +/- 9.963    [infer_isize] skewness: 0.006; kurtosis: -0.099; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.67 sec    [bwa_sai2sam_pe_core] changing coordinates of 5340 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 840 out of 840 Q17 singletons are mated.    [bwa_paired_sw] 12 out of 13 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.11 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.43 sec    [bwa_sai2sam_pe_core] print alignments... 1.81 sec    [bwa_sai2sam_pe_core] 6029312 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 244004 pairs: 199.527 +/- 9.940    [infer_isize] skewness: -0.004; kurtosis: -0.090; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.58 sec    [bwa_sai2sam_pe_core] changing coordinates of 5332 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 874 out of 874 Q17 singletons are mated.    [bwa_paired_sw] 14 out of 17 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.12 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.87 sec    [bwa_sai2sam_pe_core] 6291456 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243871 pairs: 199.521 +/- 9.953    [infer_isize] skewness: 0.002; kurtosis: -0.090; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.76 sec    [bwa_sai2sam_pe_core] changing coordinates of 5438 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 849 out of 849 Q17 singletons are mated.    [bwa_paired_sw] 10 out of 14 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.11 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.92 sec    [bwa_sai2sam_pe_core] 6553600 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243984 pairs: 199.469 +/- 9.936    [infer_isize] skewness: -0.001; kurtosis: -0.087; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.55 sec    [bwa_sai2sam_pe_core] changing coordinates of 5204 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 872 out of 872 Q17 singletons are mated.    [bwa_paired_sw] 10 out of 13 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.11 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.91 sec    [bwa_sai2sam_pe_core] 6815744 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243821 pairs: 199.507 +/- 9.948    [infer_isize] skewness: 0.004; kurtosis: -0.088; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.72 sec    [bwa_sai2sam_pe_core] changing coordinates of 5387 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 821 out of 821 Q17 singletons are mated.    [bwa_paired_sw] 12 out of 13 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.11 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.90 sec    [bwa_sai2sam_pe_core] 7077888 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 244057 pairs: 199.468 +/- 9.932    [infer_isize] skewness: -0.001; kurtosis: -0.100; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.51 sec    [bwa_sai2sam_pe_core] changing coordinates of 5473 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 819 out of 819 Q17 singletons are mated.    [bwa_paired_sw] 10 out of 10 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.11 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.92 sec    [bwa_sai2sam_pe_core] 7340032 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243999 pairs: 199.497 +/- 9.932    [infer_isize] skewness: 0.003; kurtosis: -0.098; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.64 sec    [bwa_sai2sam_pe_core] changing coordinates of 5273 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 846 out of 846 Q17 singletons are mated.    [bwa_paired_sw] 9 out of 12 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.11 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.91 sec    [bwa_sai2sam_pe_core] 7602176 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 244005 pairs: 199.491 +/- 9.930    [infer_isize] skewness: -0.001; kurtosis: -0.113; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.10 sec    [bwa_sai2sam_pe_core] changing coordinates of 5347 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 830 out of 830 Q17 singletons are mated.    [bwa_paired_sw] 17 out of 20 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.11 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.43 sec    [bwa_sai2sam_pe_core] print alignments... 1.81 sec    [bwa_sai2sam_pe_core] 7864320 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243487 pairs: 199.504 +/- 9.930    [infer_isize] skewness: 0.003; kurtosis: -0.096; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.73 sec    [bwa_sai2sam_pe_core] changing coordinates of 5565 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 846 out of 846 Q17 singletons are mated.    [bwa_paired_sw] 23 out of 23 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.11 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.91 sec    [bwa_sai2sam_pe_core] 8126464 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243895 pairs: 199.494 +/- 9.962    [infer_isize] skewness: -0.002; kurtosis: -0.096; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.54 sec    [bwa_sai2sam_pe_core] changing coordinates of 5427 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 831 out of 831 Q17 singletons are mated.    [bwa_paired_sw] 18 out of 18 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.11 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.91 sec    [bwa_sai2sam_pe_core] 8388608 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243919 pairs: 199.499 +/- 9.956    [infer_isize] skewness: -0.005; kurtosis: -0.084; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.73 sec    [bwa_sai2sam_pe_core] changing coordinates of 5456 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 847 out of 847 Q17 singletons are mated.    [bwa_paired_sw] 14 out of 15 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.12 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.90 sec    [bwa_sai2sam_pe_core] 8650752 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243745 pairs: 199.521 +/- 9.947    [infer_isize] skewness: 0.002; kurtosis: -0.076; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.68 sec    [bwa_sai2sam_pe_core] changing coordinates of 5409 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 862 out of 862 Q17 singletons are mated.    [bwa_paired_sw] 21 out of 22 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.11 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.45 sec    [bwa_sai2sam_pe_core] print alignments... 1.91 sec    [bwa_sai2sam_pe_core] 8912896 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 199, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 243763 pairs: 199.499 +/- 9.938    [infer_isize] skewness: -0.005; kurtosis: -0.101; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 7.43 sec    [bwa_sai2sam_pe_core] changing coordinates of 5403 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 870 out of 870 Q17 singletons are mated.    [bwa_paired_sw] 13 out of 14 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.11 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.43 sec    [bwa_sai2sam_pe_core] print alignments... 1.81 sec    [bwa_sai2sam_pe_core] 9175040 sequences have been processed.    [bwa_sai2sam_pe_core] convert to sequence coordinate...     [infer_isize] (25, 50, 75) percentile: (193, 200, 206)    [infer_isize] low and high boundaries: 167 and 232 for estimating avg and std    [infer_isize] inferred external isize from 75635 pairs: 199.481 +/- 9.970    [infer_isize] skewness: -0.015; kurtosis: -0.109; ap_prior: 1.00e-05    [infer_isize] inferred maximum insert size: 266 (6.70 sigma)    [bwa_sai2sam_pe_core] time elapses: 2.59 sec    [bwa_sai2sam_pe_core] changing coordinates of 1651 alignments.    [bwa_sai2sam_pe_core] align unmapped mate...    [bwa_paired_sw] 259 out of 259 Q17 singletons are mated.    [bwa_paired_sw] 3 out of 3 Q17 discordant pairs are fixed.    [bwa_sai2sam_pe_core] time elapses: 0.05 sec    [bwa_sai2sam_pe_core] refine gapped alignments... 0.14 sec    [bwa_sai2sam_pe_core] print alignments... 0.59 sec    [bwa_sai2sam_pe_core] 9256331 sequences have been processed.    [main] Version: 0.7.13-r1126    [main] CMD: bwa sampe GRCH38BWAindex/GRCH38chr1L3556522.fasta g38L100c10000000Nhs20Paired1.sai g38L100c10000000Nhs20Paired2.sai g38L100c10000000Nhs20Paired1.fq g38L100c10000000Nhs20Paired2.fq    [main] Real time: 562.819 sec; CPU: 386.586 sec

参考

【1】https://github.com/xubo245/AdamLearning【2】https://github.com/bigdatagenomics/adam/ 【3】https://github.com/xubo245/SparkLearning【4】http://spark.apache.org

研究成果：

【1】 [BIBM] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Chao Wang, and Xuehai Zhou, "Distributed Gene Clinical Decision Support System Based on Cloud Computing", in IEEE International Conference on Bioinformatics and Biomedicine. (BIBM 2017, CCF B)【2】 [IEEE CLOUD] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Xuehai Zhou. Efficient Distributed Smith-Waterman Algorithm Based on Apache Spark (CLOUD 2017, CCF-C).【3】 [CCGrid] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Jinhong Zhou, Xuehai Zhou. DSA: Scalable Distributed Sequence Alignment System Using SIMD Instructions. (CCGrid 2017, CCF-C).【4】more: https://github.com/xubo245/Publications

Help

If you have any questions or suggestions, please write it in the issue of this project or send an e-mail to me: [e-mail]: xu601450868QQ: 601450868