유전자 데이터 처리 58의 snap 운행paired-end (1천만 개의 100bp의reads 쌍)
8579 단어 유전자 데이터 처리
hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ snap-aligner index GRCH38BWAindex/GRCH38chr1L3556522.fasta snapindex
Welcome to SNAP version 1.0beta.23.
Hash table slack 0.300000
Loading FASTA file 'GRCH38BWAindex/GRCH38chr1L3556522.fasta' into memory...
FASTA file contained a character that's not a valid base (or N): 'M', full line 'TCACCCCCCACACACACCAAACAMCCCACACAACACACACACACCACACCACACAAACACAAACACACCA';
converting to 'N'. This may happen again, but there will be no more warnings.
5s
Saving genome...0s
Computing bias table.
Bias computation: 100000000 / 248957422
Bias computation: 200000000 / 248957422
Computed bias table in 10s
Allocating memory for hash tables...3s
Building hash tables.
Indexing 100000000 / 248957422
Indexing 200000000 / 248957422
7173030(2%) seeds occur more than once, total of 45140283(18%) genome locations are not unique, 18478659(7%) bad seeds, 0 both complements used 500 no string
Hash table build took 38s
Building overflow table.
Overflow table build and hash table save took 19s
Saving overflow table...0s
Index build and save took 76s (3275755 bases/s)
hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ snap-aligner paired snapindex g38L100c10000000Nhs20Paired1.
g38L100c10000000Nhs20Paired1.aln g38L100c10000000Nhs20Paired1.fq g38L100c10000000Nhs20Paired1.sai
hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ snap-aligner paired snapindex g38L100c10000000Nhs20Paired1.fq g38L100c10000000Nhs20Paired2.fq -o g38L100c10000000Nhs20Paired12.snap.sam
Welcome to SNAP version 1.0beta.23.
Loading index from directory... 0s. 248957422 bases, seed size 20
Aligning.
Total Reads Aligned, MAPQ >= 10 Aligned, MAPQ < 10 Unaligned Too Short/Too Many Ns %Pairs Reads/s Time in Aligner (s)
18,512,662 18,007,468 (97.27%) 502,480 (2.71%) 2,714 (0.01%) 0 (0.00%) 99.95% 47,683 388
hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ cat g38L100c10000000Nhs20Paired12.snap.sam |wc -l
18512666
두번째
hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ snap-aligner paired snap/snapindex g38L100c10000000Nhs20Paired1.fq g38L100c10000000Nhs20Paired2.fq -o snap/g38L100c10000000Nhs20Paired12.snap2.sam
Welcome to SNAP version 1.0beta.23.
Loading index from directory... 12s. 248957422 bases, seed size 20
Aligning.
Total Reads Aligned, MAPQ >= 10 Aligned, MAPQ < 10 Unaligned Too Short/Too Many Ns %Pairs Reads/s Time in Aligner (s)
18,512,662 18,007,468 (97.27%) 502,480 (2.71%) 2,714 (0.01%) 0 (0.00%) 99.95% 47,020 394
참고 자료
【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
연구 결과:
【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
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유전자 데이터 처리 77 vcf 파일에서 어떤 염색체의 데이터 추출1. 코드: 2. 스크립트: 3. 결과: GRCH38chr20: GRCH38chr22:...
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