基因数据处理64之bwamem处理500bp和1000bp的记录

xubo@xubo:~/xubo/data/alignment/cs-bwamem$ bwa mem bwaindex/GRCH38chr1L3556522.fasta g38l500N10000.fq >g38l500N10000.bwamem.sam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 10000 sequences (5000000 bp)...
[M::mem_process_seqs] Processed 10000 reads in 20.158 CPU sec, 20.183 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /home/xubo/xubo/tools/bwa-0.7.12/bwa mem bwaindex/GRCH38chr1L3556522.fasta g38l500N10000.fq
[main] Real time: 26.217 sec; CPU: 20.800 sec
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ samtools g38l500N10000.bwamem.sam 
[main] unrecognized command 'g38l500N10000.bwamem.sam'
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ samtools flagstatg38l500N10000.bwamem.sam 
[main] unrecognized command 'flagstatg38l500N10000.bwamem.sam'
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ samtools flagstat g38l500N10000.bwamem.sam 
10000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10000 + 0 mapped (100.00% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ bwa mem bwaindex/GRCH38chr1L3556522.fasta g38l5000N10000.fq >g38l500N100000.bwamem.sam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[E::main_mem] fail to open file `g38l5000N10000.fq'.
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ bwa mem bwaindex/GRCH38chr1L3556522.fasta g38l500N100000.fq >g38l500N100000.bwamem.sam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 20000 sequences (10000000 bp)...
[M::process] read 20000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 20000 reads in 41.470 CPU sec, 41.454 real sec
[M::process] read 20000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 20000 reads in 40.513 CPU sec, 40.457 real sec
[M::process] read 20000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 20000 reads in 41.056 CPU sec, 40.989 real sec
[M::process] read 20000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 20000 reads in 42.112 CPU sec, 42.049 real sec
[M::mem_process_seqs] Processed 20000 reads in 41.096 CPU sec, 41.084 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /home/xubo/xubo/tools/bwa-0.7.12/bwa mem bwaindex/GRCH38chr1L3556522.fasta g38l500N100000.fq
[main] Real time: 206.985 sec; CPU: 206.697 sec
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ samtools flagstat g38l500N100000.bwamem.sam 
100000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
100000 + 0 mapped (100.00% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ bwa mem bwaindex/GRCH38chr1L3556522.fasta g38l1000N10000.fq >g38l1000N10000.bwamem.sam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 10000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 10000 reads in 57.290 CPU sec, 57.343 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /home/xubo/xubo/tools/bwa-0.7.12/bwa mem bwaindex/GRCH38chr1L3556522.fasta g38l1000N10000.fq
[main] Real time: 58.228 sec; CPU: 57.736 sec
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ samtools flagstat g38l1000N10000.bwamem.sam 
10000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10000 + 0 mapped (100.00% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ bwa mem bwaindex/GRCH38chr1L3556522.fasta g38l1000N100000.fq >g38l1000N100000.bwamem.sam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 10000 sequences (10000000 bp)...
[M::process] read 10000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 10000 reads in 55.334 CPU sec, 55.333 real sec
[M::process] read 10000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 10000 reads in 57.380 CPU sec, 57.341 real sec
[M::process] read 10000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 10000 reads in 56.189 CPU sec, 56.150 real sec
[M::process] read 10000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 10000 reads in 59.506 CPU sec, 59.470 real sec
[M::process] read 10000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 10000 reads in 57.034 CPU sec, 56.994 real sec
[M::process] read 10000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 10000 reads in 58.887 CPU sec, 58.849 real sec
[M::process] read 10000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 10000 reads in 57.591 CPU sec, 57.553 real sec
[M::process] read 10000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 10000 reads in 55.443 CPU sec, 55.412 real sec
[M::process] read 10000 sequences (10000000 bp)...
[M::mem_process_seqs] Processed 10000 reads in 56.343 CPU sec, 56.304 real sec
[M::mem_process_seqs] Processed 10000 reads in 58.834 CPU sec, 58.846 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /home/xubo/xubo/tools/bwa-0.7.12/bwa mem bwaindex/GRCH38chr1L3556522.fasta g38l1000N100000.fq
[main] Real time: 573.158 sec; CPU: 572.982 sec
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ samtools flagstat g38l1000N100000.bwamem.sam 
100000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
100000 + 0 mapped (100.00% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

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
【5】http://stackoverflow.com/questions/28166667/how-to-pass-d-parameter-or-environment-variable-to-spark-job  
【6】http://stackoverflow.com/questions/28840438/how-to-override-sparks-log4j-properties-per-driver

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: [email protected]
Wechat: xu601450868
QQ: 601450868