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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,n...|125166941|125167041|   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|
|[chr1,248956422,n...|125181832|125181932|   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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,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|
|[chr1,248956422,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

(2)合并前后数据展示:

hadoop@Master:~$ hadoop fs -du -h /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/0
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/1
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/10
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/100
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/101
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/102
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/103
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/104
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/105
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/106
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/107
9.6 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/108
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/109
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/11
9.7 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/110
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/111
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/112
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/113
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/114
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/115
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/116
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/117
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/118
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/119
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/12
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/120
10.1 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/121
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/122
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/123
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/124
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/125
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/126
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/127
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/128
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/129
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/13
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/130
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/131
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/132
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/133
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/134
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/135
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/136
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/137
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/138
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/139
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/14
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/140
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/141
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/142
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/143
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/144
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/145
10.1 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/146
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/147
1.6 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/148
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/15
9.7 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/16
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/17
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/18
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/19
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/2
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/20
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/21
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/22
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/23
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/24
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/25
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/26
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/27
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/28
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/29
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/3
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/30
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/31
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/32
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/33
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/34
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/35
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/36
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/37
10.1 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/38
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/39
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/4
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/40
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/41
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9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/5
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/50
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9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/58
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/59
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/6
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10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/70
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9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/95
10.0 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/96
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/97
9.9 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/98
9.8 M   /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.adam/99
hadoop@Master:~$ hadoop fs -du -h /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.merge.adam
du: `/xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.merge.adam': No such file or directory
hadoop@Master:~$ hadoop fs -du -h /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.merge.adam
0      /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.merge.adam/_SUCCESS
9.7 K  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.merge.adam/_common_metadata
1.6 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.merge.adam/_metadata
4.2 M  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.merge.adam/part-r-00000.gz.parquet
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