基因数据处理8之BWA_MEM小数据集处理（成功）

基因数据处理8之BWA_MEM小数据集处理

环境：ubuntu14.04 6G内存

参考基因：GRCH38 来源请参考【1】

1.fastq数据：SRR003161.fastq 的头20行，即5条reads

操作记录：

hadoop@Master:~/cloud/adam/xubo/data/test20160310$ cat SRR003161.fastq |head -20 >SRR003161h20.fastq
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ wc -l SRR003161*
         0 SRR003161a.sam
       350 SRR003161b.sam
^C
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ 
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ wc -l SRR003161h20.fastq 
20 SRR003161h20.fastq
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ bwa mem GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h20.fastq >SRR003161h20.sam
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[M::process] read 5 sequences (2691 bp)...
[M::mem_process_seqs] Processed 5 reads in 0.283 CPU sec,30.784 real sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa mem GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h20.fastq
[main] Real time: 312.605 sec; CPU: 8.826 sec
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ ls
GCA_000001405.15_GRCh38  SRR003161a.sam  SRR003161b.sam  SRR003161.fastq  SRR003161.fastq.gz  SRR003161h20.fastq  SRR003161h20.sam  SRR003161.sai
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ cat SRR003161h20.sam 
@SQ	SN:chr1	LN:248956422
@SQ	SN:chr2	LN:242193529
@SQ	SN:chr3	LN:198295559
@SQ	SN:chr4	LN:190214555
@SQ	SN:chr5	LN:181538259
@SQ	SN:chr6	LN:170805979
@SQ	SN:chr7	LN:159345973
@SQ	SN:chr8	LN:145138636
@SQ	SN:chr9	LN:138394717
@SQ	SN:chr10	LN:133797422
@SQ	SN:chr11	LN:135086622
@SQ	SN:chr12	LN:133275309
@SQ	SN:chr13	LN:114364328
@SQ	SN:chr14	LN:107043718
@SQ	SN:chr15	LN:101991189
@SQ	SN:chr16	LN:90338345
@SQ	SN:chr17	LN:83257441
@SQ	SN:chr18	LN:80373285
@SQ	SN:chr19	LN:58617616
@SQ	SN:chr20	LN:64444167
@SQ	SN:chr21	LN:46709983
@SQ	SN:chr22	LN:50818468
@SQ	SN:chrX	LN:156040895
@SQ	SN:chrY	LN:57227415
@SQ	SN:chrM	LN:16569
@SQ	SN:chr1_KI270706v1_random	LN:175055
@SQ	SN:chr1_KI270707v1_random	LN:32032
@SQ	SN:chr1_KI270708v1_random	LN:127682
@SQ	SN:chr1_KI270709v1_random	LN:66860
@SQ	SN:chr1_KI270710v1_random	LN:40176
@SQ	SN:chr1_KI270711v1_random	LN:42210
@SQ	SN:chr1_KI270712v1_random	LN:176043
@SQ	SN:chr1_KI270713v1_random	LN:40745
@SQ	SN:chr1_KI270714v1_random	LN:41717
@SQ	SN:chr2_KI270715v1_random	LN:161471
@SQ	SN:chr2_KI270716v1_random	LN:153799
@SQ	SN:chr3_GL000221v1_random	LN:155397
@SQ	SN:chr4_GL000008v2_random	LN:209709
@SQ	SN:chr5_GL000208v1_random	LN:92689
@SQ	SN:chr9_KI270717v1_random	LN:40062
@SQ	SN:chr9_KI270718v1_random	LN:38054
@SQ	SN:chr9_KI270719v1_random	LN:176845
@SQ	SN:chr9_KI270720v1_random	LN:39050
@SQ	SN:chr11_KI270721v1_random	LN:100316
@SQ	SN:chr14_GL000009v2_random	LN:201709
@SQ	SN:chr14_GL000225v1_random	LN:211173
@SQ	SN:chr14_KI270722v1_random	LN:194050
@SQ	SN:chr14_GL000194v1_random	LN:191469
@SQ	SN:chr14_KI270723v1_random	LN:38115
@SQ	SN:chr14_KI270724v1_random	LN:39555
@SQ	SN:chr14_KI270725v1_random	LN:172810
@SQ	SN:chr14_KI270726v1_random	LN:43739
@SQ	SN:chr15_KI270727v1_random	LN:448248
@SQ	SN:chr16_KI270728v1_random	LN:1872759
@SQ	SN:chr17_GL000205v2_random	LN:185591
@SQ	SN:chr17_KI270729v1_random	LN:280839
@SQ	SN:chr17_KI270730v1_random	LN:112551
@SQ	SN:chr22_KI270731v1_random	LN:150754
@SQ	SN:chr22_KI270732v1_random	LN:41543
@SQ	SN:chr22_KI270733v1_random	LN:179772
@SQ	SN:chr22_KI270734v1_random	LN:165050
@SQ	SN:chr22_KI270735v1_random	LN:42811
@SQ	SN:chr22_KI270736v1_random	LN:181920
@SQ	SN:chr22_KI270737v1_random	LN:103838
@SQ	SN:chr22_KI270738v1_random	LN:99375
@SQ	SN:chr22_KI270739v1_random	LN:73985
@SQ	SN:chrY_KI270740v1_random	LN:37240
@SQ	SN:chrUn_KI270302v1	LN:2274
@SQ	SN:chrUn_KI270304v1	LN:2165
@SQ	SN:chrUn_KI270303v1	LN:1942
@SQ	SN:chrUn_KI270305v1	LN:1472
@SQ	SN:chrUn_KI270322v1	LN:21476
@SQ	SN:chrUn_KI270320v1	LN:4416
@SQ	SN:chrUn_KI270310v1	LN:1201
@SQ	SN:chrUn_KI270316v1	LN:1444
@SQ	SN:chrUn_KI270315v1	LN:2276
@SQ	SN:chrUn_KI270312v1	LN:998
@SQ	SN:chrUn_KI270311v1	LN:12399
@SQ	SN:chrUn_KI270317v1	LN:37690
@SQ	SN:chrUn_KI270412v1	LN:1179
@SQ	SN:chrUn_KI270411v1	LN:2646
@SQ	SN:chrUn_KI270414v1	LN:2489
@SQ	SN:chrUn_KI270419v1	LN:1029
@SQ	SN:chrUn_KI270418v1	LN:2145
@SQ	SN:chrUn_KI270420v1	LN:2321
@SQ	SN:chrUn_KI270424v1	LN:2140
@SQ	SN:chrUn_KI270417v1	LN:2043
@SQ	SN:chrUn_KI270422v1	LN:1445
@SQ	SN:chrUn_KI270423v1	LN:981
@SQ	SN:chrUn_KI270425v1	LN:1884
@SQ	SN:chrUn_KI270429v1	LN:1361
@SQ	SN:chrUn_KI270442v1	LN:392061
@SQ	SN:chrUn_KI270466v1	LN:1233
@SQ	SN:chrUn_KI270465v1	LN:1774
@SQ	SN:chrUn_KI270467v1	LN:3920
@SQ	SN:chrUn_KI270435v1	LN:92983
@SQ	SN:chrUn_KI270438v1	LN:112505
@SQ	SN:chrUn_KI270468v1	LN:4055
@SQ	SN:chrUn_KI270510v1	LN:2415
@SQ	SN:chrUn_KI270509v1	LN:2318
@SQ	SN:chrUn_KI270518v1	LN:2186
@SQ	SN:chrUn_KI270508v1	LN:1951
@SQ	SN:chrUn_KI270516v1	LN:1300
@SQ	SN:chrUn_KI270512v1	LN:22689
@SQ	SN:chrUn_KI270519v1	LN:138126
@SQ	SN:chrUn_KI270522v1	LN:5674
@SQ	SN:chrUn_KI270511v1	LN:8127
@SQ	SN:chrUn_KI270515v1	LN:6361
@SQ	SN:chrUn_KI270507v1	LN:5353
@SQ	SN:chrUn_KI270517v1	LN:3253
@SQ	SN:chrUn_KI270529v1	LN:1899
@SQ	SN:chrUn_KI270528v1	LN:2983
@SQ	SN:chrUn_KI270530v1	LN:2168
@SQ	SN:chrUn_KI270539v1	LN:993
@SQ	SN:chrUn_KI270538v1	LN:91309
@SQ	SN:chrUn_KI270544v1	LN:1202
@SQ	SN:chrUn_KI270548v1	LN:1599
@SQ	SN:chrUn_KI270583v1	LN:1400
@SQ	SN:chrUn_KI270587v1	LN:2969
@SQ	SN:chrUn_KI270580v1	LN:1553
@SQ	SN:chrUn_KI270581v1	LN:7046
@SQ	SN:chrUn_KI270579v1	LN:31033
@SQ	SN:chrUn_KI270589v1	LN:44474
@SQ	SN:chrUn_KI270590v1	LN:4685
@SQ	SN:chrUn_KI270584v1	LN:4513
@SQ	SN:chrUn_KI270582v1	LN:6504
@SQ	SN:chrUn_KI270588v1	LN:6158
@SQ	SN:chrUn_KI270593v1	LN:3041
@SQ	SN:chrUn_KI270591v1	LN:5796
@SQ	SN:chrUn_KI270330v1	LN:1652
@SQ	SN:chrUn_KI270329v1	LN:1040
@SQ	SN:chrUn_KI270334v1	LN:1368
@SQ	SN:chrUn_KI270333v1	LN:2699
@SQ	SN:chrUn_KI270335v1	LN:1048
@SQ	SN:chrUn_KI270338v1	LN:1428
@SQ	SN:chrUn_KI270340v1	LN:1428
@SQ	SN:chrUn_KI270336v1	LN:1026
@SQ	SN:chrUn_KI270337v1	LN:1121
@SQ	SN:chrUn_KI270363v1	LN:1803
@SQ	SN:chrUn_KI270364v1	LN:2855
@SQ	SN:chrUn_KI270362v1	LN:3530
@SQ	SN:chrUn_KI270366v1	LN:8320
@SQ	SN:chrUn_KI270378v1	LN:1048
@SQ	SN:chrUn_KI270379v1	LN:1045
@SQ	SN:chrUn_KI270389v1	LN:1298
@SQ	SN:chrUn_KI270390v1	LN:2387
@SQ	SN:chrUn_KI270387v1	LN:1537
@SQ	SN:chrUn_KI270395v1	LN:1143
@SQ	SN:chrUn_KI270396v1	LN:1880
@SQ	SN:chrUn_KI270388v1	LN:1216
@SQ	SN:chrUn_KI270394v1	LN:970
@SQ	SN:chrUn_KI270386v1	LN:1788
@SQ	SN:chrUn_KI270391v1	LN:1484
@SQ	SN:chrUn_KI270383v1	LN:1750
@SQ	SN:chrUn_KI270393v1	LN:1308
@SQ	SN:chrUn_KI270384v1	LN:1658
@SQ	SN:chrUn_KI270392v1	LN:971
@SQ	SN:chrUn_KI270381v1	LN:1930
@SQ	SN:chrUn_KI270385v1	LN:990
@SQ	SN:chrUn_KI270382v1	LN:4215
@SQ	SN:chrUn_KI270376v1	LN:1136
@SQ	SN:chrUn_KI270374v1	LN:2656
@SQ	SN:chrUn_KI270372v1	LN:1650
@SQ	SN:chrUn_KI270373v1	LN:1451
@SQ	SN:chrUn_KI270375v1	LN:2378
@SQ	SN:chrUn_KI270371v1	LN:2805
@SQ	SN:chrUn_KI270448v1	LN:7992
@SQ	SN:chrUn_KI270521v1	LN:7642
@SQ	SN:chrUn_GL000195v1	LN:182896
@SQ	SN:chrUn_GL000219v1	LN:179198
@SQ	SN:chrUn_GL000220v1	LN:161802
@SQ	SN:chrUn_GL000224v1	LN:179693
@SQ	SN:chrUn_KI270741v1	LN:157432
@SQ	SN:chrUn_GL000226v1	LN:15008
@SQ	SN:chrUn_GL000213v1	LN:164239
@SQ	SN:chrUn_KI270743v1	LN:210658
@SQ	SN:chrUn_KI270744v1	LN:168472
@SQ	SN:chrUn_KI270745v1	LN:41891
@SQ	SN:chrUn_KI270746v1	LN:66486
@SQ	SN:chrUn_KI270747v1	LN:198735
@SQ	SN:chrUn_KI270748v1	LN:93321
@SQ	SN:chrUn_KI270749v1	LN:158759
@SQ	SN:chrUn_KI270750v1	LN:148850
@SQ	SN:chrUn_KI270751v1	LN:150742
@SQ	SN:chrUn_KI270752v1	LN:27745
@SQ	SN:chrUn_KI270753v1	LN:62944
@SQ	SN:chrUn_KI270754v1	LN:40191
@SQ	SN:chrUn_KI270755v1	LN:36723
@SQ	SN:chrUn_KI270756v1	LN:79590
@SQ	SN:chrUn_KI270757v1	LN:71251
@SQ	SN:chrUn_GL000214v1	LN:137718
@SQ	SN:chrUn_KI270742v1	LN:186739
@SQ	SN:chrUn_GL000216v2	LN:176608
@SQ	SN:chrUn_GL000218v1	LN:161147
@SQ	SN:chr1_KI270762v1_alt	LN:354444
@SQ	SN:chr1_KI270766v1_alt	LN:256271
@SQ	SN:chr1_KI270760v1_alt	LN:109528
@SQ	SN:chr1_KI270765v1_alt	LN:185285
@SQ	SN:chr1_GL383518v1_alt	LN:182439
@SQ	SN:chr1_GL383519v1_alt	LN:110268
@SQ	SN:chr1_GL383520v2_alt	LN:366580
@SQ	SN:chr1_KI270764v1_alt	LN:50258
@SQ	SN:chr1_KI270763v1_alt	LN:911658
@SQ	SN:chr1_KI270759v1_alt	LN:425601
@SQ	SN:chr1_KI270761v1_alt	LN:165834
@SQ	SN:chr2_KI270770v1_alt	LN:136240
@SQ	SN:chr2_KI270773v1_alt	LN:70887
@SQ	SN:chr2_KI270774v1_alt	LN:223625
@SQ	SN:chr2_KI270769v1_alt	LN:120616
@SQ	SN:chr2_GL383521v1_alt	LN:143390
@SQ	SN:chr2_KI270772v1_alt	LN:133041
@SQ	SN:chr2_KI270775v1_alt	LN:138019
@SQ	SN:chr2_KI270771v1_alt	LN:110395
@SQ	SN:chr2_KI270768v1_alt	LN:110099
@SQ	SN:chr2_GL582966v2_alt	LN:96131
@SQ	SN:chr2_GL383522v1_alt	LN:123821
@SQ	SN:chr2_KI270776v1_alt	LN:174166
@SQ	SN:chr2_KI270767v1_alt	LN:161578
@SQ	SN:chr3_JH636055v2_alt	LN:173151
@SQ	SN:chr3_KI270783v1_alt	LN:109187
@SQ	SN:chr3_KI270780v1_alt	LN:224108
@SQ	SN:chr3_GL383526v1_alt	LN:180671
@SQ	SN:chr3_KI270777v1_alt	LN:173649
@SQ	SN:chr3_KI270778v1_alt	LN:248252
@SQ	SN:chr3_KI270781v1_alt	LN:113034
@SQ	SN:chr3_KI270779v1_alt	LN:205312
@SQ	SN:chr3_KI270782v1_alt	LN:162429
@SQ	SN:chr3_KI270784v1_alt	LN:184404
@SQ	SN:chr4_KI270790v1_alt	LN:220246
@SQ	SN:chr4_GL383528v1_alt	LN:376187
@SQ	SN:chr4_KI270787v1_alt	LN:111943
@SQ	SN:chr4_GL000257v2_alt	LN:586476
@SQ	SN:chr4_KI270788v1_alt	LN:158965
@SQ	SN:chr4_GL383527v1_alt	LN:164536
@SQ	SN:chr4_KI270785v1_alt	LN:119912
@SQ	SN:chr4_KI270789v1_alt	LN:205944
@SQ	SN:chr4_KI270786v1_alt	LN:244096
@SQ	SN:chr5_KI270793v1_alt	LN:126136
@SQ	SN:chr5_KI270792v1_alt	LN:179043
@SQ	SN:chr5_KI270791v1_alt	LN:195710
@SQ	SN:chr5_GL383532v1_alt	LN:82728
@SQ	SN:chr5_GL949742v1_alt	LN:226852
@SQ	SN:chr5_KI270794v1_alt	LN:164558
@SQ	SN:chr5_GL339449v2_alt	LN:1612928
@SQ	SN:chr5_GL383530v1_alt	LN:101241
@SQ	SN:chr5_KI270796v1_alt	LN:172708
@SQ	SN:chr5_GL383531v1_alt	LN:173459
@SQ	SN:chr5_KI270795v1_alt	LN:131892
@SQ	SN:chr6_GL000250v2_alt	LN:4672374
@SQ	SN:chr6_KI270800v1_alt	LN:175808
@SQ	SN:chr6_KI270799v1_alt	LN:152148
@SQ	SN:chr6_GL383533v1_alt	LN:124736
@SQ	SN:chr6_KI270801v1_alt	LN:870480
@SQ	SN:chr6_KI270802v1_alt	LN:75005
@SQ	SN:chr6_KB021644v2_alt	LN:185823
@SQ	SN:chr6_KI270797v1_alt	LN:197536
@SQ	SN:chr6_KI270798v1_alt	LN:271782
@SQ	SN:chr7_KI270804v1_alt	LN:157952
@SQ	SN:chr7_KI270809v1_alt	LN:209586
@SQ	SN:chr7_KI270806v1_alt	LN:158166
@SQ	SN:chr7_GL383534v2_alt	LN:119183
@SQ	SN:chr7_KI270803v1_alt	LN:1111570
@SQ	SN:chr7_KI270808v1_alt	LN:271455
@SQ	SN:chr7_KI270807v1_alt	LN:126434
@SQ	SN:chr7_KI270805v1_alt	LN:209988
@SQ	SN:chr8_KI270818v1_alt	LN:145606
@SQ	SN:chr8_KI270812v1_alt	LN:282736
@SQ	SN:chr8_KI270811v1_alt	LN:292436
@SQ	SN:chr8_KI270821v1_alt	LN:985506
@SQ	SN:chr8_KI270813v1_alt	LN:300230
@SQ	SN:chr8_KI270822v1_alt	LN:624492
@SQ	SN:chr8_KI270814v1_alt	LN:141812
@SQ	SN:chr8_KI270810v1_alt	LN:374415
@SQ	SN:chr8_KI270819v1_alt	LN:133535
@SQ	SN:chr8_KI270820v1_alt	LN:36640
@SQ	SN:chr8_KI270817v1_alt	LN:158983
@SQ	SN:chr8_KI270816v1_alt	LN:305841
@SQ	SN:chr8_KI270815v1_alt	LN:132244
@SQ	SN:chr9_GL383539v1_alt	LN:162988
@SQ	SN:chr9_GL383540v1_alt	LN:71551
@SQ	SN:chr9_GL383541v1_alt	LN:171286
@SQ	SN:chr9_GL383542v1_alt	LN:60032
@SQ	SN:chr9_KI270823v1_alt	LN:439082
@SQ	SN:chr10_GL383545v1_alt	LN:179254
@SQ	SN:chr10_KI270824v1_alt	LN:181496
@SQ	SN:chr10_GL383546v1_alt	LN:309802
@SQ	SN:chr10_KI270825v1_alt	LN:188315
@SQ	SN:chr11_KI270832v1_alt	LN:210133
@SQ	SN:chr11_KI270830v1_alt	LN:177092
@SQ	SN:chr11_KI270831v1_alt	LN:296895
@SQ	SN:chr11_KI270829v1_alt	LN:204059
@SQ	SN:chr11_GL383547v1_alt	LN:154407
@SQ	SN:chr11_JH159136v1_alt	LN:200998
@SQ	SN:chr11_JH159137v1_alt	LN:191409
@SQ	SN:chr11_KI270827v1_alt	LN:67707
@SQ	SN:chr11_KI270826v1_alt	LN:186169
@SQ	SN:chr12_GL877875v1_alt	LN:167313
@SQ	SN:chr12_GL877876v1_alt	LN:408271
@SQ	SN:chr12_KI270837v1_alt	LN:40090
@SQ	SN:chr12_GL383549v1_alt	LN:120804
@SQ	SN:chr12_KI270835v1_alt	LN:238139
@SQ	SN:chr12_GL383550v2_alt	LN:169178
@SQ	SN:chr12_GL383552v1_alt	LN:138655
@SQ	SN:chr12_GL383553v2_alt	LN:152874
@SQ	SN:chr12_KI270834v1_alt	LN:119498
@SQ	SN:chr12_GL383551v1_alt	LN:184319
@SQ	SN:chr12_KI270833v1_alt	LN:76061
@SQ	SN:chr12_KI270836v1_alt	LN:56134
@SQ	SN:chr13_KI270840v1_alt	LN:191684
@SQ	SN:chr13_KI270839v1_alt	LN:180306
@SQ	SN:chr13_KI270843v1_alt	LN:103832
@SQ	SN:chr13_KI270841v1_alt	LN:169134
@SQ	SN:chr13_KI270838v1_alt	LN:306913
@SQ	SN:chr13_KI270842v1_alt	LN:37287
@SQ	SN:chr14_KI270844v1_alt	LN:322166
@SQ	SN:chr14_KI270847v1_alt	LN:1522222
@SQ	SN:chr14_KI270845v1_alt	LN:180703
@SQ	SN:chr14_KI270846v1_alt	LN:1351393
@SQ	SN:chr15_KI270852v1_alt	LN:478999
@SQ	SN:chr15_KI270851v1_alt	LN:263054
@SQ	SN:chr15_KI270848v1_alt	LN:327382
@SQ	SN:chr15_GL383554v1_alt	LN:296527
@SQ	SN:chr15_KI270849v1_alt	LN:244917
@SQ	SN:chr15_GL383555v2_alt	LN:388773
@SQ	SN:chr15_KI270850v1_alt	LN:430880
@SQ	SN:chr16_KI270854v1_alt	LN:134193
@SQ	SN:chr16_KI270856v1_alt	LN:63982
@SQ	SN:chr16_KI270855v1_alt	LN:232857
@SQ	SN:chr16_KI270853v1_alt	LN:2659700
@SQ	SN:chr16_GL383556v1_alt	LN:192462
@SQ	SN:chr16_GL383557v1_alt	LN:89672
@SQ	SN:chr17_GL383563v3_alt	LN:375691
@SQ	SN:chr17_KI270862v1_alt	LN:391357
@SQ	SN:chr17_KI270861v1_alt	LN:196688
@SQ	SN:chr17_KI270857v1_alt	LN:2877074
@SQ	SN:chr17_JH159146v1_alt	LN:278131
@SQ	SN:chr17_JH159147v1_alt	LN:70345
@SQ	SN:chr17_GL383564v2_alt	LN:133151
@SQ	SN:chr17_GL000258v2_alt	LN:1821992
@SQ	SN:chr17_GL383565v1_alt	LN:223995
@SQ	SN:chr17_KI270858v1_alt	LN:235827
@SQ	SN:chr17_KI270859v1_alt	LN:108763
@SQ	SN:chr17_GL383566v1_alt	LN:90219
@SQ	SN:chr17_KI270860v1_alt	LN:178921
@SQ	SN:chr18_KI270864v1_alt	LN:111737
@SQ	SN:chr18_GL383567v1_alt	LN:289831
@SQ	SN:chr18_GL383570v1_alt	LN:164789
@SQ	SN:chr18_GL383571v1_alt	LN:198278
@SQ	SN:chr18_GL383568v1_alt	LN:104552
@SQ	SN:chr18_GL383569v1_alt	LN:167950
@SQ	SN:chr18_GL383572v1_alt	LN:159547
@SQ	SN:chr18_KI270863v1_alt	LN:167999
@SQ	SN:chr19_KI270868v1_alt	LN:61734
@SQ	SN:chr19_KI270865v1_alt	LN:52969
@SQ	SN:chr19_GL383573v1_alt	LN:385657
@SQ	SN:chr19_GL383575v2_alt	LN:170222
@SQ	SN:chr19_GL383576v1_alt	LN:188024
@SQ	SN:chr19_GL383574v1_alt	LN:155864
@SQ	SN:chr19_KI270866v1_alt	LN:43156
@SQ	SN:chr19_KI270867v1_alt	LN:233762
@SQ	SN:chr19_GL949746v1_alt	LN:987716
@SQ	SN:chr20_GL383577v2_alt	LN:128386
@SQ	SN:chr20_KI270869v1_alt	LN:118774
@SQ	SN:chr20_KI270871v1_alt	LN:58661
@SQ	SN:chr20_KI270870v1_alt	LN:183433
@SQ	SN:chr21_GL383578v2_alt	LN:63917
@SQ	SN:chr21_KI270874v1_alt	LN:166743
@SQ	SN:chr21_KI270873v1_alt	LN:143900
@SQ	SN:chr21_GL383579v2_alt	LN:201197
@SQ	SN:chr21_GL383580v2_alt	LN:74653
@SQ	SN:chr21_GL383581v2_alt	LN:116689
@SQ	SN:chr21_KI270872v1_alt	LN:82692
@SQ	SN:chr22_KI270875v1_alt	LN:259914
@SQ	SN:chr22_KI270878v1_alt	LN:186262
@SQ	SN:chr22_KI270879v1_alt	LN:304135
@SQ	SN:chr22_KI270876v1_alt	LN:263666
@SQ	SN:chr22_KI270877v1_alt	LN:101331
@SQ	SN:chr22_GL383583v2_alt	LN:96924
@SQ	SN:chr22_GL383582v2_alt	LN:162811
@SQ	SN:chrX_KI270880v1_alt	LN:284869
@SQ	SN:chrX_KI270881v1_alt	LN:144206
@SQ	SN:chr19_KI270882v1_alt	LN:248807
@SQ	SN:chr19_KI270883v1_alt	LN:170399
@SQ	SN:chr19_KI270884v1_alt	LN:157053
@SQ	SN:chr19_KI270885v1_alt	LN:171027
@SQ	SN:chr19_KI270886v1_alt	LN:204239
@SQ	SN:chr19_KI270887v1_alt	LN:209512
@SQ	SN:chr19_KI270888v1_alt	LN:155532
@SQ	SN:chr19_KI270889v1_alt	LN:170698
@SQ	SN:chr19_KI270890v1_alt	LN:184499
@SQ	SN:chr19_KI270891v1_alt	LN:170680
@SQ	SN:chr1_KI270892v1_alt	LN:162212
@SQ	SN:chr2_KI270894v1_alt	LN:214158
@SQ	SN:chr2_KI270893v1_alt	LN:161218
@SQ	SN:chr3_KI270895v1_alt	LN:162896
@SQ	SN:chr4_KI270896v1_alt	LN:378547
@SQ	SN:chr5_KI270897v1_alt	LN:1144418
@SQ	SN:chr5_KI270898v1_alt	LN:130957
@SQ	SN:chr6_GL000251v2_alt	LN:4795265
@SQ	SN:chr7_KI270899v1_alt	LN:190869
@SQ	SN:chr8_KI270901v1_alt	LN:136959
@SQ	SN:chr8_KI270900v1_alt	LN:318687
@SQ	SN:chr11_KI270902v1_alt	LN:106711
@SQ	SN:chr11_KI270903v1_alt	LN:214625
@SQ	SN:chr12_KI270904v1_alt	LN:572349
@SQ	SN:chr15_KI270906v1_alt	LN:196384
@SQ	SN:chr15_KI270905v1_alt	LN:5161414
@SQ	SN:chr17_KI270907v1_alt	LN:137721
@SQ	SN:chr17_KI270910v1_alt	LN:157099
@SQ	SN:chr17_KI270909v1_alt	LN:325800
@SQ	SN:chr17_JH159148v1_alt	LN:88070
@SQ	SN:chr17_KI270908v1_alt	LN:1423190
@SQ	SN:chr18_KI270912v1_alt	LN:174061
@SQ	SN:chr18_KI270911v1_alt	LN:157710
@SQ	SN:chr19_GL949747v2_alt	LN:729520
@SQ	SN:chr22_KB663609v1_alt	LN:74013
@SQ	SN:chrX_KI270913v1_alt	LN:274009
@SQ	SN:chr19_KI270914v1_alt	LN:205194
@SQ	SN:chr19_KI270915v1_alt	LN:170665
@SQ	SN:chr19_KI270916v1_alt	LN:184516
@SQ	SN:chr19_KI270917v1_alt	LN:190932
@SQ	SN:chr19_KI270918v1_alt	LN:123111
@SQ	SN:chr19_KI270919v1_alt	LN:170701
@SQ	SN:chr19_KI270920v1_alt	LN:198005
@SQ	SN:chr19_KI270921v1_alt	LN:282224
@SQ	SN:chr19_KI270922v1_alt	LN:187935
@SQ	SN:chr19_KI270923v1_alt	LN:189352
@SQ	SN:chr3_KI270924v1_alt	LN:166540
@SQ	SN:chr4_KI270925v1_alt	LN:555799
@SQ	SN:chr6_GL000252v2_alt	LN:4604811
@SQ	SN:chr8_KI270926v1_alt	LN:229282
@SQ	SN:chr11_KI270927v1_alt	LN:218612
@SQ	SN:chr19_GL949748v2_alt	LN:1064304
@SQ	SN:chr22_KI270928v1_alt	LN:176103
@SQ	SN:chr19_KI270929v1_alt	LN:186203
@SQ	SN:chr19_KI270930v1_alt	LN:200773
@SQ	SN:chr19_KI270931v1_alt	LN:170148
@SQ	SN:chr19_KI270932v1_alt	LN:215732
@SQ	SN:chr19_KI270933v1_alt	LN:170537
@SQ	SN:chr19_GL000209v2_alt	LN:177381
@SQ	SN:chr3_KI270934v1_alt	LN:163458
@SQ	SN:chr6_GL000253v2_alt	LN:4677643
@SQ	SN:chr19_GL949749v2_alt	LN:1091841
@SQ	SN:chr3_KI270935v1_alt	LN:197351
@SQ	SN:chr6_GL000254v2_alt	LN:4827813
@SQ	SN:chr19_GL949750v2_alt	LN:1066390
@SQ	SN:chr3_KI270936v1_alt	LN:164170
@SQ	SN:chr6_GL000255v2_alt	LN:4606388
@SQ	SN:chr19_GL949751v2_alt	LN:1002683
@SQ	SN:chr3_KI270937v1_alt	LN:165607
@SQ	SN:chr6_GL000256v2_alt	LN:4929269
@SQ	SN:chr19_GL949752v1_alt	LN:987100
@SQ	SN:chr6_KI270758v1_alt	LN:76752
@SQ	SN:chr19_GL949753v2_alt	LN:796479
@SQ	SN:chr19_KI270938v1_alt	LN:1066800
@SQ	SN:chrEBV	LN:171823
@PG	ID:bwa	PN:bwa	VN:0.7.13-r1126	CL:bwa mem GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h20.fastq
SRR003161.1	0	chr1	143217889	0	4S35M85S	*	0	0	TCAGATGCAATCATCGAATGGTCTCGAATGGAATCNTCTANAGAGATGGAATGTATCNCTCGCCANACGACACNCGAACAGGGNAAGGCAAGCAGNAGGNAGNNNANNNNNNNNNNNNNNNNNN	AAAAAAAAAAAAAAAA:::BAAFAABAAB?>>=44!39=<!:866699888220862!08:8002!0200000!022200800!20660000600!000!06!!!6!!!!!!!!!!!!!!!!!!	NM:i:1	MD:Z:31A3	AS:i:3XS:i:33	XA:Z:chr10,+42092546,4S35M85S,1;chr1,+143217421,+143239587,-143252938,85S35M4S,+143220601,+143219665,-143210830,1;chr10,+42075371,+42101425,+143272381,-143204112,+143189975,+42080829,+42067652,+143236600,+42071261,+143202568,+143262016,+42094445,+143229991,+143194906,+42098197,+143229325,+143273144,+143236132,1;chr3,-196898795,-125173710,+42074903,+143193143,+143190443,+42085796,+143224622,+143267943,+42103854,+143225093,-143249828,+143231300,-143256486,-143209440,+143228021,+143185063,-41852367,-143251629,+143233540,+42093977,+143200517,+143194441,+42070793,+143206914,+143237811,+143227553,-143255189,+143231768,+143271341,+42080361,+143213870,+42074435,+143263324,+42097745,+42090276,-125180284,+143240055,+143265756,+143216113,-125169985,+143219197,+143192675,+42095848,+143195374,+143214338,+143270772,-125166285,+143275099,+143226451,+42104319,+143232233,+143211626,+143220133,+143215645,+42100036,-41846998,-125168084,-125179816,+143240523,+143264771,+143212094,4S34M86S,-41845898,86S34M4S,+143191375,4S31M89S,0;chr1,-125182919,89S31M4S,+143221908,+143190911,0;chr10,-41843753,0;chr10_KI270824v1_alt,+1080,1;chr10_KI270824v1_alt,+615,1;
SRR003161.2	0	chr7	41381016	60	4S153M1D132M1D5M1D28M1D73M3I12M1I40M54S	*	0	0	TCAGTTTGAGATGGAGTTTCATTCTTGTTGCCCAGGCTGGAGTGCAATGGCGCAATCTCAGCTCACAGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCTCGAGTAGCTGGGATTACAGGCATGCACCATCACGCCCAGCTAATTTGCATTTTTTATTAGAGATGGGGTTTCTCCACATTGGTCAGGCTGATCTCGAACTCCTGACCTCAGGTGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCTGAGCCCAACCTATTTACTTTCAATCCATCTTTTCAATAACTTAAATACAAGTGTCAATATATACAATCTTTTCCTCCCTGGTTATCAAGCTTTCTAATATATATGGATGTATCTTCCAAGGTTTTTGATCCCATTTTACTTTACAGGCTCACTGCTGTGGAACCCAGAGAGCAGTCTCTTTTCAAGGNGGGCTGAGACNCGCAACAGGGGATTAGGCCAAGGCNCAGG	CCCCCCCCCCCCCCCC@@@CCCFEEEFEEG888EEEFFEEEEFGGGGGGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA<777@@CCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAAACCCCCCCCCCCCCCCCCCCCCCC:93339@A>77//39AC666666C22CAAAA93333///7-0017>9999>>A???ACCCCCCC2239322>9977<?????CCCCCCCCC877777777222221::::5555:555:::::::::;:555:;;::::0040-----***--467::::;;;;;;:::511155555:555:::;::::::7777744-------///245::;;;::::::;;;;;;;;:55554774----------44-----064---------6---522451115247644255-----,4---24464422---------!,4464224!11:::7:::222221--7777---!----	NM:i:1MD:Z:153^T40T91^T5^T28^G73G23C0G26	AS:i:379	XS:i:88
SRR003161.3	0	chr7	59292897	0	4S28M1I35M577S	*	0	0	TCAGCATGCTAGACAGAAGAATTCTCAGTAACTTTCTTTGTGCTGTGTGTATTCAACTCACAGAGTTGGAACCGTTCCTTTGTCAACAGAGCTAGAATTTGAAACCNCTCTTGAGGACTACGCGAAANAGGGGANAAGGTCCAAAGGCCAGTANAGGGNTCGGANGTANAAGATNCTNAAAATAAAACNGANAGAATCATTCTNAAGAAACTTNTTGNATGTNTGCCCTTTCAAACTCAACAGGAGTTTACCAAACCTTTTCTTTTCTAAAGGAGACTAAGGTTTTAAGAAAACCACTTACTCGGTCTTTGGTTAATGTCTGCAAAGGTGGATTATTGGACCTTCTTGAGGTCCCTTTCGTTGCGTAAAACCGGGGTTTCTTCCTTTCACTTAGTCGTACGTAACGTAAACGTAAAAGGTAAAGGTTACGTTACGTTAACGTTTAAACGTTTTTTTAACGTTTTGGTTTGGTTTGGTTGTTAGTTTACTTAACCTTAACCTAACCTAAACGTAAAGGTTTAACGGTTAAACCGTTAACGTTACGTTTAACGTTAAGGTAAGGAAGGACGAGTAAGTTAAGTTAAACTAAACTACTAGTAGACGACGACAACGAAGGAGAGAGAGACGACACGAGGAGGAGNGNNN	AAAAAAAAAAAAAAAAAAAAAAIFAABA?7792222.,:3<<<<:0222276:220::20020028662222022000002,220006666=9000669600000!0699788...4877873...!,.333.!......4447........!....!....4!...!..66.!..!....4+++*.!..!.33333686--!---------!--3!332,!,*,2,.,((((,(,),..000----,)),10,1,1..,03330,)))),0(((,100,-03,----)))),'''',(((,))),))00,000,11133-,-,10000,!!!	NM:i:1	MD:Z:63	AS:i:56	XS:i:56
SRR003161.4	0	chr6	71805157	60	4S88M495S	*	0	0	TCAGGTTTGGAATGTGGGCTCTGAAGCCATACAACACAGTTTCTACTCTTTATCTTACACCTCCTGACTTTGTGACATTGGTTAAATATTTTATTTATTATNNCATAACTTACTACTTTGTTAAATTAGAAGTACGACTGTCTACACTCTTAGGTAGTTGGTCTGTTGAAATTAAATAATAGNACTTTAACTTACTTAAATAGANATACACACGACTTAGTTAGTTGTTGGCTGGAAATTAGGTATNTGTTTTAGTTCCTACACCTTACTTAACCCTAACCTACCATNTAATACTTTTACTTGTTCTCNGANANATNATAGTNTCTACGTTGAGTATATTACTTATATTACACGGTACGACGGACCGACGTCGTACACGTCTCGTCTTCTNCNANNATGTAGTGAGTCTNTTTATTNTTTCTTAACTACTACTACTCGTTGTAGTAAGTAATAATAANTNNTCTACACCTACGACTGTATTGTAAGTACAAGAAGGACCGACGTTTCGTTACCTTTCTTCTTCGTCCTCTACTTAACCTGTTACTACGTACGCGAACACGGACGTAGGAGGAGGAGGACACGAACGG	AAAAAAAAAAAAAAAAAAAAAAIEEAIIIIIIAAIIIA:666AAE???<<<@AA===A=>>AAAAAAAAAAAAA?@???980000040....0/**04490!!00000600.........,.....,.....74..............33.....7.....4..............++664!.000000.135855----*--!3------------33,2222222,3,((,00,01!333001,03((,433,13,04,!!,311,1))!,30,0330,003333,0003,01,033,1331313/.,010,3303,0000000,03,34333,NM:i:0	MD:Z:88	AS:i:88	XS:i:20
SRR003161.5	4	*	0	0	*	*	0	0	TCAGATGAATGGAGTGGATGGAGTTGAGTGGAATGGAATGGAATGGATGGAGTGGAATTGGAAGTAGTANAGGTNTTGAATGGATGGAATGGATATAGAGGAATGGATGGATGATGGANGTAGNGAGTGAGTAGGAGTACGNGTAGGTACCGTGGAGTTGGGAAGTGTTANAGAGTAAGGNTTGGAGGTAGGTTTGTTAGGTAAAGNGTTACCGGTAAGGTAGGTGGTAAAGTAGGGGGAAAATTTGGGTAAAGGGGTGGGTAAACCGTAGTGGAAAAACCCTTACGGGCGTAAAACGNGGGGGGGAAAATTTAGGGGGGGGTACCCTAAAAGGGGGGGTAACGTAACGGGAAAAACTAGGGGGGGGGTAAATTAAAGGGGGAGAGGAGGTGGGTAAGTAGGTAAAAGTAGGGAGGTGTAAAGTAGGGAGTGGGTAGTAGGGAAATGGGGTAAAAGTGGGGGGTAAAAAGTTTAGGAGGTTTTTAAGGTAGGGAAGGTAAGTAAAAGTAGGGGTAAAAGTAGGGTAGGGTAGGGAAAGTGGGGTAAATTTAGGGGTAGTAGGGGTAAAAGTAGGGTATTTAGGGGGTATAACGGGGTTAGGGGAAGGGTTAGGGTAAGTAAGGTAAGTAGGGAAGTAGGGTAGGTAGGTAGGTTAGGGTAAGTAGGGTAAGGAAGAAGGTAGGGTAAAGTAGGGTAAAGTAGGTAAAGGGTAAGGGTAGTAGGGTAGGTAGGGTAGGTTTTTAGGTAGGTAGGGTAAAAAAAGGTGGTAAAGGTAGGGTAAAGTGGGTAGGGTAGGTAAAAAAAGGGTGTAAGTTTTTAGTAGTTTTAGG	AAAAAAAAAAAAAAA446=BAA????B?E????@@BB@B::::?A=<93220;::22222288:85666!0222!00222<<<<96666690000000000009:999777;666;;;!4483!34...............!.............4744.....,....4!3433.....!..44........---*.3-------!-33------3855,252,8.333444470003/.,11-3,33),0.65565..!//222,--,',/////..33.,)(,000101,-22,00----33)...,33,33-)),)1...,..,(30----0,/0--2,)))110,030/..00,10.,0)),/32,)0,))))),))0,(300,))30,3/,./,3----------0),00)30,AS:i:0	XS:i:0
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ cat SRR003161h20.sam |wc -l
462
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ cat SRR003161h20.sam 

2.fastq数据：SRR003161.fastq 的头1000行，即250条reads

hadoop@Master:~/cloud/adam/xubo/data/test20160310$ cat SRR003161.fastq |head -1000 >SRR003161h1000.fastq
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ bwa mem GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h1000.fastq >SRR003161h1000.sam
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[M::process] read 250 sequences (161179 bp)...
[M::mem_process_seqs] Processed 250 reads in 10.963 CPU sec,1525.205 real sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa mem GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h1000.fastq
[main] Real time: 1805.888 sec; CPU: 18.755 sec
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ wc -l SRR003161h1000.*
  1000 SRR003161h1000.fastq
   734 SRR003161h1000.sam
  1734 total
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ cat SRR003161h1000.sam |head -10
@SQ	SN:chr1	LN:248956422
@SQ	SN:chr2	LN:242193529
@SQ	SN:chr3	LN:198295559
@SQ	SN:chr4	LN:190214555
@SQ	SN:chr5	LN:181538259
@SQ	SN:chr6	LN:170805979
@SQ	SN:chr7	LN:159345973
@SQ	SN:chr8	LN:145138636
@SQ	SN:chr9	LN:138394717
@SQ	SN:chr10	LN:133797422

3.fastq数据：SRR003161.fastq 的头10000行，即2500条reads

hadoop@Master:~/cloud/adam/xubo/data/test20160310$ cat SRR003161.fastq |head -10000 >SRR003161h10000.fastq
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ bwa mem GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h10000.fastq >SRR003161h10000.sam
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[M::process] read 2500 sequences (1499370 bp)...
[M::mem_process_seqs] Processed 2500 reads in 55.162 CPU sec,6750.093 real sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa mem GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h10000.fastq
[main] Real time: 7224.315 sec; CPU: 69.348 sec
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ cat SRR003161h1000* |wc -l
14798
hadoop@Master:~/cloud/adam/xubo/data/test20160310$ wc -l SRR003161h1000* 
  10000 SRR003161h10000.fastq
   3064 SRR003161h10000.sam
   1000 SRR003161h1000.fastq
    734 SRR003161h1000.sam
  14798 total

【1】?http://blog.csdn.net/xubo245/article/details/50858334