基因数据处理52之cs-bwamem集群版运行（1千万条100bp的reads）

1.art生成模拟序列：

art_illumina -ss HS20 -i GRCH38BWAindex/GRCH38chr1L3556522.fna -l 100 -c 10000000 -o g38L100c10000000Nhs20

2.上传到hdfs，制定partition数

spark-submit  --class cs.ucla.edu.bwaspark.BWAMEMSpark --master spark://masterIP:7077  /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/cloud-scale-bwamem-0.2.0-assembly.jar upload-fastq   0 21 g38L100c10000000Nhs20.fq /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.fastq

masterIP为真实IP

3.使用cs-bwamem进行匹配

spark-submit --executor-memory 4g --class cs.ucla.edu.bwaspark.BWAMEMSpark --total-executor-cores 20 --master spark://masterIP:7077  --conf spark.driver.host=masterIP --conf spark.driver.cores=4 --conf spark.driver.maxResultSize=4g --conf spark.storage.memoryFraction=0.7  --conf spark.akka.threads=2 --conf spark.akka.frameSize=1024 /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/cloud-scale-bwamem-0.2.0-assembly.jar cs-bwamem -bfn 1 -bPSW 1 -sbatch 10 -bPSWJNI 1  -oChoice 2 -oPath hdfs://masterIP:9000/xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam -localRef 1  -isSWExtBatched 1  0 GRCH38BWAindex/GRCH38chr1L3556522.fasta  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.fastq

4.将数据进行合并

spark-submit --executor-memory 4g --class cs.ucla.edu.bwaspark.BWAMEMSpark --total-executor-cores 4 --master spark://masterIP:7077  --conf spark.driver.host=masterIP --conf spark.driver.cores=4 --conf spark.driver.maxResultSize=6g --conf spark.storage.memoryFraction=0.7  --conf spark.akka.threads=2 --conf spark.akka.frameSize=1024 /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/cloud-scale-bwamem-0.2.0-assembly.jar merge hdfs://masterIP:9000 /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.merge.adam

5.统计数量
行数：34253515
distinct:34253515

分析：distinct显示没有重复的数据
问题：distinct耗时太长，本地得30分钟

参考：

https://github.com/ytchen0323/cloud-scale-bwamem/blob/453a4178cd6c3fb3a0fe99df816e6cd7df521b95/src/main/scala/cs/ucla/edu/bwaspark/Usage.scala

附录：
（1）部分df。show：

+--------------------+---------+---------+----+------------+--------------------+--------------------+-----+---------------------+-------------------+----------+----------+----------+----------+-----------+------------+-------------------------+-------------+------------------+------------------+----------------+------------------+----------------------+--------------------+--------+--------------------+---------------+---------------------------+----------------------+-----------------------+--------------------+----------------------+------------------+------------------------------------+-------------------+-----------------------+-----------------+------------------+----------------+----------+
| contig| start| end|mapq| readName| sequence| qual|cigar|basesTrimmedFromStart|basesTrimmedFromEnd|readPaired|properPair|readMapped|mateMapped|firstOfPair|secondOfPair|failedVendorQualityChecks|duplicateRead|readNegativeStrand|mateNegativeStrand|primaryAlignment|secondaryAlignment|supplementaryAlignment|mismatchingPositions|origQual| attributes|recordGroupName|recordGroupSequencingCenter|recordGroupDescription|recordGroupRunDateEpoch|recordGroupFlowOrder|recordGroupKeySequence|recordGroupLibrary|recordGroupPredictedMedianInsertSize|recordGroupPlatform|recordGroupPlatformUnit|recordGroupSample|mateAlignmentStart|mateAlignmentEnd|mateContig|
+--------------------+---------+---------+----+------------+--------------------+--------------------+-----+---------------------+-------------------+----------+----------+----------+----------+-----------+------------+-------------------------+-------------+------------------+------------------+----------------+------------------+----------------------+--------------------+--------+--------------------+---------------+---------------------------+----------------------+-----------------------+--------------------+----------------------+------------------+------------------------------------+-------------------+-----------------------+-----------------+------------------+----------------+----------+
|[chr1,248956422,n...| 14809719| 14809819|  60|chr1-6811129|CATGTACAGTGCTCGCC...|CEDA8DA@E<DDED.DE...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| true| false| true| false| false|            34T46C18| null|NM:i:2    AS:i:90 XS...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...| 80256345| 80256445|  60|chr1-6811128|AGTAGGCTTGGAGAAGA...|D?BCED>D=@DDEC9CF...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| true| false| true| false| false|                 100| null|NM:i:0    AS:i:100    X...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|173354132|173354232|  60|chr1-6811126|AGCACAATCAGAAATAA...|?@@FFDFF2?HHHJ3JJ...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| false| false| true| false| false|               29T70| null|NM:i:1    AS:i:95 XS...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...| 67191506| 67191606|  60|chr1-6811125|CATTCCCATTGGCTTTT...|?C@F=DEFHHHHHFHIH...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| false| false| true| false| false|                 100| null|NM:i:0    AS:i:100    X...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|143209655|143209755|   5|chr1-6811124|ATTCCATTTGATGACAA...|D5>D:DBCCAC5>,(AC...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| true| false| true| false| false|            31A44C23| null|NM:i:2    AS:i:90 XS...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|125183587|125183687|   0|chr1-6811124|ATTCCATTTGATGACAA...|D5>D:DBCCAC5>,(AC...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| true| false| false| true| false|          31A0A43C23| null|NM:i:3    AS:i:85 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|125166941|125167041|   0|chr1-6811124|ATTCCATTTGATGACAA...|D5>D:DBCCAC5>,n...|125181832|125181932|   0|chr1-6811124|ATTCCATTTGATGACAA...|D5>D:DBCCAC5>,n...|143271137|143271237|   0|chr1-6811124|TGGAATCATGATCAAAT...|C@CFFFFDGH:HAJJIJ...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| false| false| false| true| false|          23G43T0T31| null|NM:i:3    AS:i:85 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|143211045|143211145|   0|chr1-6811124|ATTCCATTTGATGACAA...|D5>D:DBCCAC5>,(AC...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| true| false| false| true| false|        27A3A0A43C23| null|NM:i:4    AS:i:80 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|143189224|143189324|   0|chr1-6811124|TGGAATCATGATCAAAT...|C@CFFFFDGH:HAJJIJ...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| false| false| false| true| false|       23G22G20T0T31| null|NM:i:4    AS:i:80 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|143233259|143233359|   0|chr1-6811124|TGGAATCATGATCAAAT...|C@CFFFFDGH:HAJJIJ...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| false| false| false| true| false|        6T16G43T0T31| null|NM:i:4    AS:i:80 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|143274817|143274917|   0|chr1-6811124|TGGAATCATGATCAAAT...|C@CFFFFDGH:HAJJIJ...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| false| false| false| true| false|       23G14T28T0T31| null|NM:i:4    AS:i:80 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|143215364|143215464|   0|chr1-6811124|TGGAATCATGATCAAAT...|C@CFFFFDGH:HAJJIJ...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| false| false| false| true| false|        6T16G43T0T31| null|NM:i:4    AS:i:80 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|125180499|125180599|   0|chr1-6811124|ATTCCATTTGATGACAA...|D5>D:DBCCAC5>,(AC...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| true| false| false| true| false|        31A0A43C16A6| null|NM:i:4    AS:i:80 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|143267274|143267374|   0|chr1-6811124|TGGAATCATGATCAAAT...|C@CFFFFDGH:HAJJIJ...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| false| false| false| true| false|        6T16G43T0T31| null|NM:i:4    AS:i:80 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|143226169|143226269|   0|chr1-6811124|TGGAATCATGATCAAAT...|C@CFFFFDGH:HAJJIJ...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| false| false| false| true| false|       23G14T28T0T31| null|NM:i:4    AS:i:80 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|143264022|143264122|   0|chr1-6811124|TGGAATCATGATCAAAT...|C@CFFFFDGH:HAJJIJ...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| false| false| false| true| false|        6T16G43T0T31| null|NM:i:4    AS:i:80 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|143223869|143223969|   0|chr1-6811124|TGGAATCATGATCAAAT...|C@CFFFFDGH:HAJJIJ...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| false| false| false| true| false|       23G25C17T0T31| null|NM:i:4    AS:i:80 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
|[chr1,n...|143258530|143258630|   0|chr1-6811124|ATTCCATTTGATGACAA...|D5>D:DBCCAC5>,(AC...| 100M|                    0|                  0| false| false| true| false| false| false| false| false| true| false| false| true| false|       31A0A17G25C23| null|NM:i:4    AS:i:80 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null|
+--------------------+---------+---------+----+------------+--------------------+--------------------+-----+---------------------+-------------------+----------+----------+----------+----------+-----------+------------+-------------------------+-------------+------------------+------------------+----------------+------------------+----------------------+--------------------+--------+--------------------+---------------+---------------------------+----------------------+-----------------------+--------------------+----------------------+------------------+------------------------------------+-------------------+-----------------------+-----------------+------------------+----------------+----------+
only showing top 20 rows

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