基因数据处理13之bwa处理SRR003161

基因数据处理13之bwa处理SRR003161

hadoop@Master:~/cloud/adam/xubo/data/test20160310$ bwa aln GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161.fastq >SRR003161.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... 689.79 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 698.87 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 596.52 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... 612.55 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 618.69 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 141.51 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1376701 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161.fastq
[main] Real time: 3681.828 sec; CPU: 3369.765 sec

hadoop@Master:~/cloud/adam/xubo/data/test20160310$ bwa samse GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161.sai SRR003161.fastq >SRR003161bwa.sam
[bwa_aln_core] convert to sequence coordinate... 6.30 sec
[bwa_aln_core] refine gapped alignments... 2.40 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.25 sec
[bwa_aln_core] refine gapped alignments... 2.24 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.35 sec
[bwa_aln_core] refine gapped alignments... 1.81 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.57 sec
[bwa_aln_core] refine gapped alignments... 1.68 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.04 sec
[bwa_aln_core] refine gapped alignments... 1.74 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.29 sec
[bwa_aln_core] refine gapped alignments... 0.83 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 1376701 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161.sai SRR003161.fastq
[main] Real time: 1710.215 sec; CPU: 59.919 sec

hadoop@Master:~/cloud/adam/xubo/data/test20160310$ wc -l SRR003161bwa.sam
1377158 SRR003161bwa.sam
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ wc -l SRR003161.fastq
5506804 SRR003161.fastq
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ ll -h
total 3.7G
drwxrwxr-x 3 hadoop hadoop 4.0K  3月 13 17:43 ./
drwxrwxr-x 3 hadoop hadoop 4.0K  3月 12 14:51 ../
drwxrwxr-x 2 hadoop hadoop 4.0K  3月 13 15:49 GCA_000001405.15_GRCh38/
-rw-rw-r-- 1 hadoop hadoop 1.6G  3月 13 18:12 SRR003161bwa.sam
-rw-rw-r-- 1 hadoop hadoop 1.6G  3月 12 15:49 SRR003161.fastq
-rw-rw-r-- 1 hadoop hadoop 527M  3月 12 16:10 SRR003161.fastq.gz
-rw-rw-r-- 1 hadoop hadoop  29M  3月 13 16:38 SRR003161h100000bwa.sam
-rw-rw-r-- 1 hadoop hadoop  30M  3月 13 16:31 SRR003161h100000.fastq
-rw-rw-r-- 1 hadoop hadoop 106K  3月 13 16:34 SRR003161h100000.sai
-rw-rw-r-- 1 hadoop hadoop 3.0M  3月 13 15:01 SRR003161h10000bwa.sam
-rw-rw-r-- 1 hadoop hadoop 3.1M  3月 12 22:50 SRR003161h10000.fastq
-rw-rw-r-- 1 hadoop hadoop  11K  3月 13 14:46 SRR003161h10000.sai
-rw-rw-r-- 1 hadoop hadoop 3.3M  3月 13 00:50 SRR003161h10000.sam
-rw-rw-r-- 1 hadoop hadoop 339K  3月 13 15:28 SRR003161h1000bwa.sam
-rw-rw-r-- 1 hadoop hadoop 336K  3月 12 22:08 SRR003161h1000.fastq
-rw-rw-r-- 1 hadoop hadoop 1.1K  3月 13 14:41 SRR003161h1000.sai
-rw-rw-r-- 1 hadoop hadoop 9.8K  3月 13 15:46 SRR003161h20.bam
-rw-rw-r-- 1 hadoop hadoop  22K  3月 13 15:23 SRR003161h20bwa.sam
-rw-rw-r-- 1 hadoop hadoop 5.7K  3月 13 15:20 SRR003161h20.fastq
-rw-rw-r-- 1 hadoop hadoop   88  3月 13 15:21 SRR003161h20.sai
-rw-rw-r-- 1 hadoop hadoop  25K  3月 12 22:02 SRR003161h20.sam
-rw-rw-r-- 1 hadoop hadoop 9.9K  3月 13 15:47 SRR003161h20Sorted.bam
-rw-rw-r-- 1 hadoop hadoop 135K  3月 13 15:47 SRR003161h20Sorted.bam.bai
-rw-rw-r-- 1 hadoop hadoop 5.7M  3月 13 17:40 SRR003161.sai

可视化：
参考【1】

具体效果暂不列出来。

参考

【1】 http://blog.csdn.net/xubo245/article/details/50836185