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
参考【1】
具体效果暂不列出来。
参考
【1】 http://blog.csdn.net/xubo245/article/details/50836185
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