基因数据处理26之avocado运行snap-basic有问题
发布时间：2021-03-06 19:16:38 所属栏目：大数据 来源：网络整理
导读：hadoop@Master:~/xubo/data/testTools/se$ avocado-submit /xubo/avocado/hs2.fq /xubo/avocado/hs38DH.fa /xubo/avocado/test20160527NUMhs2snap /home/hadoop/xubo/data/testTools/se/snap-basic.propertiesUsing SPARK_SUBMIT=/home/hadoop/cloud/spark
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hadoop@Master:~/xubo/data/testTools/se$ avocado-submit /xubo/avocado/hs2.fq /xubo/avocado/hs38DH.fa /xubo/avocado/test20160527NUMhs2snap /home/hadoop/xubo/data/testTools/se/snap-basic.properties
Using SPARK_SUBMIT=/home/hadoop/cloud/spark-1.5.2//bin/spark-submit
Command body threw exception:
java.lang.IllegalArgumentException: No input stage with name: /home/hadoop/xubo/data/testTools/se/hs2.fq
Exception in thread "main" java.lang.IllegalArgumentException: No input stage with name: /home/hadoop/xubo/data/testTools/se/hs2.fq
at org.bdgenomics.avocado.input.Input$.apply(Input.scala:57)
at org.bdgenomics.avocado.cli.Avocado$$anonfun$4.apply(Avocado.scala:208)
at org.bdgenomics.avocado.cli.Avocado$$anonfun$4.apply(Avocado.scala:208)
at org.apache.spark.rdd.Timer.time(Timer.scala:57)
at org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:207)
at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:54)
at org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:82)
at org.bdgenomics.utils.cli.BDGCommandCompanion$class.main(BDGCommand.scala:32)
at org.bdgenomics.avocado.cli.Avocado$.main(Avocado.scala:52)
at org.bdgenomics.avocado.cli.Avocado.main(Avocado.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:674)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
配置： -rw-r--r-- 3 hadoop supergroup 47052 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwamem.c
-rw-r--r-- 3 hadoop supergroup 7986 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwamem.h
-rw-r--r-- 3 hadoop supergroup 383488 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwamem.o
-rw-r--r-- 3 hadoop supergroup 5422 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwamem_extra.c
-rw-r--r-- 3 hadoop supergroup 81144 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwamem_extra.o
-rw-r--r-- 3 hadoop supergroup 17194 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwamem_pair.c
-rw-r--r-- 3 hadoop supergroup 66824 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwamem_pair.o
-rw-r--r-- 3 hadoop supergroup 29357 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwape.c
-rw-r--r-- 3 hadoop supergroup 112688 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwape.o
-rw-r--r-- 3 hadoop supergroup 19467 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwase.c
-rw-r--r-- 3 hadoop supergroup 1033 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwase.h
-rw-r--r-- 3 hadoop supergroup 88208 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwase.o
-rw-r--r-- 3 hadoop supergroup 6868 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwaseqio.c
-rw-r--r-- 3 hadoop supergroup 38560 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwaseqio.o
-rw-r--r-- 3 hadoop supergroup 5816 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwashm.c
-rw-r--r-- 3 hadoop supergroup 37928 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwashm.o
-rw-r--r-- 3 hadoop supergroup 15342 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwt.c
-rw-r--r-- 3 hadoop supergroup 4966 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwt.h
-rw-r--r-- 3 hadoop supergroup 57264 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwt.o
-rw-r--r-- 3 hadoop supergroup 53937 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwt_gen.c
-rw-r--r-- 3 hadoop supergroup 94992 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwt_gen.o
-rw-r--r-- 3 hadoop supergroup 2683 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwt_lite.c
-rw-r--r-- 3 hadoop supergroup 653 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwt_lite.h
-rw-r--r-- 3 hadoop supergroup 15232 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwt_lite.o
-rw-r--r-- 3 hadoop supergroup 11004 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtaln.c
-rw-r--r-- 3 hadoop supergroup 3833 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtaln.h
-rw-r--r-- 3 hadoop supergroup 57912 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtaln.o
-rw-r--r-- 3 hadoop supergroup 9156 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtgap.c
-rw-r--r-- 3 hadoop supergroup 999 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtgap.h
-rw-r--r-- 3 hadoop supergroup 47872 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtgap.o
-rw-r--r-- 3 hadoop supergroup 8897 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtindex.c
-rw-r--r-- 3 hadoop supergroup 50392 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtindex.o
-rw-r--r-- 3 hadoop supergroup 1524 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtsw2.h
-rw-r--r-- 3 hadoop supergroup 24964 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtsw2_aux.c
-rw-r--r-- 3 hadoop supergroup 119024 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtsw2_aux.o
-rw-r--r-- 3 hadoop supergroup 3063 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtsw2_chain.c
-rw-r--r-- 3 hadoop supergroup 33664 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtsw2_chain.o
-rw-r--r-- 3 hadoop supergroup 18955 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtsw2_core.c
-rw-r--r-- 3 hadoop supergroup 153296 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtsw2_core.o
-rw-r--r-- 3 hadoop supergroup 3818 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtsw2_main.c
-rw-r--r-- 3 hadoop supergroup 27320 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtsw2_main.o
-rw-r--r-- 3 hadoop supergroup 10337 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtsw2_pair.c
-rw-r--r-- 3 hadoop supergroup 34856 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/bwtsw2_pair.o
-rw-r--r-- 3 hadoop supergroup 1844 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/example.c
-rw-r--r-- 3 hadoop supergroup 19206 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/fastmap.c
-rw-r--r-- 3 hadoop supergroup 83696 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/fastmap.o
-rw-r--r-- 3 hadoop supergroup 6674 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/is.c
-rw-r--r-- 3 hadoop supergroup 22616 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/is.o
-rw-r--r-- 3 hadoop supergroup 15889 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/kbtree.h
-rw-r--r-- 3 hadoop supergroup 20888 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/khash.h
-rw-r--r-- 3 hadoop supergroup 9714 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/kopen.c
-rw-r--r-- 3 hadoop supergroup 50664 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/kopen.o
-rw-r--r-- 3 hadoop supergroup 8857 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/kseq.h
-rw-r--r-- 3 hadoop supergroup 9718 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/ksort.h
-rw-r--r-- 3 hadoop supergroup 703 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/kstring.c
-rw-r--r-- 3 hadoop supergroup 2332 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/kstring.h
-rw-r--r-- 3 hadoop supergroup 9272 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/kstring.o
-rw-r--r-- 3 hadoop supergroup 26112 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/ksw.c
-rw-r--r-- 3 hadoop supergroup 5091 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/ksw.h
-rw-r--r-- 3 hadoop supergroup 87312 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/ksw.o
-rw-r--r-- 3 hadoop supergroup 3611 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/kthread.c
-rw-r--r-- 3 hadoop supergroup 14688 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/kthread.o
-rw-r--r-- 3 hadoop supergroup 2940 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/kvec.h
-rw-r--r-- 3 hadoop supergroup 974790 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/libbwa.a
-rw-r--r-- 3 hadoop supergroup 4476 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/main.c
-rw-r--r-- 3 hadoop supergroup 39056 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/main.o
-rw-r--r-- 3 hadoop supergroup 1449 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/malloc_wrap.c
-rw-r--r-- 3 hadoop supergroup 1183 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/malloc_wrap.h
-rw-r--r-- 3 hadoop supergroup 13584 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/malloc_wrap.o
-rw-r--r-- 3 hadoop supergroup 8825 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/pemerge.c
-rw-r--r-- 3 hadoop supergroup 47488 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/pemerge.o
-rw-r--r-- 3 hadoop supergroup 616 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/qualfa2fq.pl
-rw-r--r-- 3 hadoop supergroup 6944 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/utils.c
-rw-r--r-- 3 hadoop supergroup 3821 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/utils.h
-rw-r--r-- 3 hadoop supergroup 87656 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/utils.o
-rw-r--r-- 3 hadoop supergroup 730 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12/xa2multi.pl
-rw-r--r-- 3 hadoop supergroup 184599 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12.tar.bz2
-rw-r--r-- 3 hadoop supergroup 184809 2016-03-07 20:34 /xubo/data/soft-gene/bwa/bwa-0.7.12.zip
-rw-r--r-- 3 hadoop supergroup 184599 2016-03-07 20:34 /xubo/data/soft-gene/bwa-0.7.12.tar.bz2
-rw-r--r-- 3 hadoop supergroup 48242521 2016-03-07 20:34 /xubo/data/soft-gene/bwakit-testonly-v2_x64-linux.tar.bz2
drwxr-xr-x - xubo supergroup 0 2016-01-26 15:50 /xubo/in1
-rw-r--r-- 3 xubo supergroup 4560 2016-01-26 15:50 /xubo/in1/English_shashibiya.txt
drwxr-xr-x - xubo supergroup 0 2016-03-28 18:45 /xubo/input
-rw-r--r-- 3 xubo supergroup 478 2016-01-26 15:35 /xubo/input/900.txt
-rw-r--r-- 3 hadoop supergroup 898235 2016-03-04 12:46 /xubo/input/SogouQ.mini
-rw-r--r-- 3 hadoop supergroup 898235 2016-03-04 12:33 /xubo/input/SogouQ.sample
-rwxrwxrwx 3 hadoop supergroup 13 2015-07-23 12:13 /xubo/input/test1.txt
-rwxrwxrwx 3 hadoop supergroup 12 2015-07-23 12:13 /xubo/input/test2.txt
drwxr-xr-x - xubo supergroup 0 2016-03-28 18:58 /xubo/input/wordcount
-rw-r--r-- 3 xubo supergroup 34 2016-03-28 18:58 /xubo/input/wordcount/0.txt
-rw-r--r-- 3 xubo supergroup 26 2016-03-28 18:46 /xubo/input/wordcount/1.txt
-rw-r--r-- 3 xubo supergroup 26 2016-03-28 18:46 /xubo/input/wordcount/2.txt
drwxr-xr-x - xubo601450868 supergroup 0 2015-07-26 22:13 /xubo/input726
-rw-r--r-- 3 xubo601450868 supergroup 12 2015-07-26 22:13 /xubo/input726/input1.txt
-rw-r--r-- 3 xubo601450868 supergroup 23 2015-07-26 22:13 /xubo/input726/input2.txt
drwxr-xr-x - hadoop supergroup 0 2016-03-16 10:54 /xubo/log
drwxr-xr-x - hadoop supergroup 0 2016-03-16 11:04 /xubo/log/bwa
-rw-r--r-- 3 hadoop supergroup 34498 2016-03-16 10:54 /xubo/log/bwa/bwaMcnode3T201603141044.txt
-rw-r--r-- 3 hadoop supergroup 20996 2016-03-16 10:54 /xubo/log/bwa/bwaMcnode3T201603141816.txt
-rw-r--r-- 3 hadoop supergroup 21053 2016-03-16 10:54 /xubo/log/bwa/bwaMcnode3T201603142234.txt
-rw-r--r-- 3 hadoop supergroup 21052 2016-03-16 10:54 /xubo/log/bwa/bwaMcnode3T201603151253.txt
-rw-r--r-- 3 hadoop supergroup 45459 2016-03-16 10:54 /xubo/log/bwa/bwaMcnode4T201603131501.txt
-rw-r--r-- 3 hadoop supergroup 20995 2016-03-16 10:54 /xubo/log/bwa/bwaMcnode4T201603141816.txt
-rw-r--r-- 3 hadoop supergroup 21052 2016-03-16 10:54 /xubo/log/bwa/bwaMcnode4T201603142234.txt
-rw-r--r-- 3 hadoop supergroup 21053 2016-03-16 10:54 /xubo/log/bwa/bwaMcnode4T201603151254.txt
drwxr-xr-x - xubo supergroup 0 2016-03-16 11:04 /xubo/log/bwa/logBwaMcnode4T201603151254.txt
-rw-r--r-- 3 xubo supergroup 0 2016-03-16 11:04 /xubo/log/bwa/logBwaMcnode4T201603151254.txt/_SUCCESS
-rw-r--r-- 3 xubo supergroup 2779 2016-03-16 11:04 /xubo/log/bwa/logBwaMcnode4T201603151254.txt/part-00000
drwxr-xr-x - hadoop supergroup 0 2016-05-04 15:51 /xubo/output
-rw-r--r-- 3 hadoop supergroup 0 2015-07-23 12:14 /xubo/output/_SUCCESS
drwxr-xr-x - hadoop supergroup 0 2016-03-28 16:45 /xubo/output/a1
-rw-r--r-- 3 hadoop supergroup 0 2016-03-28 16:45 /xubo/output/a1/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 116749 2016-03-28 16:44 /xubo/output/a1/part-00000
-rw-r--r-- 3 hadoop supergroup 123473 2016-03-28 16:44 /xubo/output/a1/part-00001
-rw-r--r-- 3 hadoop supergroup 123327 2016-03-28 16:44 /xubo/output/a1/part-00002
-rw-r--r-- 3 hadoop supergroup 121755 2016-03-28 16:45 /xubo/output/a1/part-00003
-rw-r--r-- 3 hadoop supergroup 120311 2016-03-28 16:45 /xubo/output/a1/part-00004
drwxr-xr-x - hadoop supergroup 0 2016-03-28 16:55 /xubo/output/a2
-rw-r--r-- 3 hadoop supergroup 0 2016-03-28 16:55 /xubo/output/a2/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 34671 2016-03-28 16:55 /xubo/output/a2/part-00000
-rw-r--r-- 3 hadoop supergroup 13820 2016-03-28 16:55 /xubo/output/a2/part-00001
-rw-r--r-- 3 hadoop supergroup 26687 2016-03-28 16:55 /xubo/output/a2/part-00002
-rw-r--r-- 3 hadoop supergroup 68543 2016-03-28 16:55 /xubo/output/a2/part-00003
-rw-r--r-- 3 hadoop supergroup 461894 2016-03-28 16:55 /xubo/output/a2/part-00004
drwxr-xr-x - xubo supergroup 0 2016-05-04 15:50 /xubo/output/wordcount
drwxr-xr-x - hadoop supergroup 0 2016-03-28 21:53 /xubo/output/wordcount/SparkWordCount
drwxr-xr-x - hadoop supergroup 0 2016-03-28 20:35 /xubo/output/wordcount/SparkWordCount/201603282034
-rw-r--r-- 3 hadoop supergroup 0 2016-03-28 20:35 /xubo/output/wordcount/SparkWordCount/201603282034/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 827 2016-03-28 20:35 /xubo/output/wordcount/SparkWordCount/201603282034/part-00000
-rw-r--r-- 3 hadoop supergroup 1604 2016-03-28 20:35 /xubo/output/wordcount/SparkWordCount/201603282034/part-00001
-rw-r--r-- 3 hadoop supergroup 1284 2016-03-28 20:35 /xubo/output/wordcount/SparkWordCount/201603282034/part-00002
-rw-r--r-- 3 hadoop supergroup 2373 2016-03-28 20:35 /xubo/output/wordcount/SparkWordCount/201603282034/part-00003
-rw-r--r-- 3 hadoop supergroup 16214 2016-03-28 20:35 /xubo/output/wordcount/SparkWordCount/201603282034/part-00004
-rw-r--r-- 3 hadoop supergroup 1017759 2016-03-28 20:35 /xubo/output/wordcount/SparkWordCount/201603282034/part-00005
drwxr-xr-x - hadoop supergroup 0 2016-03-28 21:54 /xubo/output/wordcount/SparkWordCount/201603282153
-rw-r--r-- 3 hadoop supergroup 0 2016-03-28 21:54 /xubo/output/wordcount/SparkWordCount/201603282153/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 827 2016-03-28 21:54 /xubo/output/wordcount/SparkWordCount/201603282153/part-00000
-rw-r--r-- 3 hadoop supergroup 1604 2016-03-28 21:54 /xubo/output/wordcount/SparkWordCount/201603282153/part-00001
-rw-r--r-- 3 hadoop supergroup 1284 2016-03-28 21:54 /xubo/output/wordcount/SparkWordCount/201603282153/part-00002
-rw-r--r-- 3 hadoop supergroup 2373 2016-03-28 21:54 /xubo/output/wordcount/SparkWordCount/201603282153/part-00003
-rw-r--r-- 3 hadoop supergroup 16214 2016-03-28 21:54 /xubo/output/wordcount/SparkWordCount/201603282153/part-00004
-rw-r--r-- 3 hadoop supergroup 1017759 2016-03-28 21:54 /xubo/output/wordcount/SparkWordCount/201603282153/part-00005
drwxr-xr-x - xubo supergroup 0 2016-03-28 18:54 /xubo/output/wordcount/WordCountSpark20160328185330944
-rw-r--r-- 3 xubo supergroup 0 2016-03-28 18:54 /xubo/output/wordcount/WordCountSpark20160328185330944/_SUCCESS
-rw-r--r-- 3 xubo supergroup 0 2016-03-28 18:53 /xubo/output/wordcount/WordCountSpark20160328185330944/part-00000
-rw-r--r-- 3 xubo supergroup 23 2016-03-28 18:53 /xubo/output/wordcount/WordCountSpark20160328185330944/part-00001
-rw-r--r-- 3 xubo supergroup 55 2016-03-28 18:54 /xubo/output/wordcount/WordCountSpark20160328185330944/part-00002
-rw-r--r-- 3 xubo supergroup 15 2016-03-28 18:54 /xubo/output/wordcount/WordCountSpark20160328185330944/part-00003
drwxr-xr-x - hadoop supergroup 0 2016-05-04 15:50 /xubo/output/wordcount/cluster
drwxr-xr-x - hadoop supergroup 0 2016-04-05 09:26 /xubo/sh
-rw-r--r-- 3 hadoop supergroup 362 2016-04-05 09:26 /xubo/sh/allrestart.sh
drwxr-xr-x - hadoop supergroup 0 2016-04-20 00:34 /xubo/spark
drwxr-xr-x - hadoop supergroup 0 2016-04-26 21:21 /xubo/spark/data
drwxr-xr-x - hadoop supergroup 0 2016-04-26 21:23 /xubo/spark/data/Streaming
drwxr-xr-x - hadoop supergroup 0 2016-04-26 21:32 /xubo/spark/data/Streaming/hdfsWordCount
-rw-r--r-- 3 hadoop supergroup 12 2016-04-26 21:26 /xubo/spark/data/Streaming/hdfsWordCount/1.txt
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-rw-r--r-- 3 xubo supergroup 12 2016-03-29 16:11 /xubo/spark/output/mllib/kmeans_data/20160329161055238/1/part-00000
drwxr-xr-x - xubo supergroup 0 2016-03-29 16:11 /xubo/spark/output/mllib/kmeans_data/20160329161055238/2
-rw-r--r-- 3 xubo supergroup 0 2016-03-29 16:11 /xubo/spark/output/mllib/kmeans_data/20160329161055238/2/_SUCCESS
-rw-r--r-- 3 xubo supergroup 84 2016-03-29 16:11 /xubo/spark/output/mllib/kmeans_data/20160329161055238/2/part-00000
drwxr-xr-x - hadoop supergroup 0 2016-03-29 16:27 /xubo/spark/output/mllib/kmeans_data/20160329162649669
drwxr-xr-x - hadoop supergroup 0 2016-03-29 16:27 /xubo/spark/output/mllib/kmeans_data/20160329162649669/1
-rw-r--r-- 3 hadoop supergroup 0 2016-03-29 16:27 /xubo/spark/output/mllib/kmeans_data/20160329162649669/1/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 12 2016-03-29 16:27 /xubo/spark/output/mllib/kmeans_data/20160329162649669/1/part-00000
drwxr-xr-x - hadoop supergroup 0 2016-03-29 16:27 /xubo/spark/output/mllib/kmeans_data/20160329162649669/2
-rw-r--r-- 3 hadoop supergroup 0 2016-03-29 16:27 /xubo/spark/output/mllib/kmeans_data/20160329162649669/2/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 84 2016-03-29 16:27 /xubo/spark/output/mllib/kmeans_data/20160329162649669/2/part-00000
drwxr-xr-x - hadoop supergroup 0 2016-03-29 16:28 /xubo/spark/output/mllib/kmeans_data/20160329162841839
drwxr-xr-x - hadoop supergroup 0 2016-03-29 16:28 /xubo/spark/output/mllib/kmeans_data/20160329162841839/1
-rw-r--r-- 3 hadoop supergroup 0 2016-03-29 16:28 /xubo/spark/output/mllib/kmeans_data/20160329162841839/1/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 12 2016-03-29 16:28 /xubo/spark/output/mllib/kmeans_data/20160329162841839/1/part-00000
drwxr-xr-x - hadoop supergroup 0 2016-03-29 16:29 /xubo/spark/output/mllib/kmeans_data/20160329162841839/2
-rw-r--r-- 3 hadoop supergroup 0 2016-03-29 16:29 /xubo/spark/output/mllib/kmeans_data/20160329162841839/2/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 84 2016-03-29 16:29 /xubo/spark/output/mllib/kmeans_data/20160329162841839/2/part-00000
drwxr-xr-x - hadoop supergroup 0 2016-04-20 00:34 /xubo/spark/people.parquet
-rw-r--r-- 3 hadoop supergroup 0 2016-04-20 00:34 /xubo/spark/people.parquet/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 277 2016-04-20 00:34 /xubo/spark/people.parquet/_common_metadata
-rw-r--r-- 3 hadoop supergroup 750 2016-04-20 00:34 /xubo/spark/people.parquet/_metadata
-rw-r--r-- 3 hadoop supergroup 537 2016-04-20 00:34 /xubo/spark/people.parquet/part-r-00000-9d377482-1bb6-46c3-bb19-d107a7da660a.gz.parquet
-rw-r--r-- 3 hadoop supergroup 531 2016-04-20 00:34 /xubo/spark/people.parquet/part-r-00001-9d377482-1bb6-46c3-bb19-d107a7da660a.gz.parquet
drwxr-xr-x - hadoop supergroup 0 2016-04-19 15:31 /xubo/tianchi
drwxr-xr-x - hadoop supergroup 0 2016-04-19 15:31 /xubo/tianchi/cainiao
drwxr-xr-x - hadoop supergroup 0 2016-04-19 15:59 /xubo/tianchi/cainiao/file
drwxr-xr-x - hadoop supergroup 0 2016-04-19 15:31 /xubo/tianchi/cainiao/file/data
drwxr-xr-x - hadoop supergroup 0 2016-04-19 15:58 /xubo/tianchi/cainiao/file/data/input
-rw-r--r-- 3 hadoop supergroup 134 2016-04-19 15:31 /xubo/tianchi/cainiao/file/data/input/cars.csv
-rw-r--r-- 3 hadoop supergroup 118835 2016-04-19 15:31 /xubo/tianchi/cainiao/file/data/input/config1.csv
drwxr-xr-x - hadoop supergroup 0 2016-04-19 15:57 /xubo/tianchi/cainiao/file/data/input/config1P.csv
-rw-r--r-- 3 hadoop supergroup 0 2016-04-19 15:57 /xubo/tianchi/cainiao/file/data/input/config1P.csv/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 346 2016-04-19 15:57 /xubo/tianchi/cainiao/file/data/input/config1P.csv/_common_metadata
-rw-r--r-- 3 hadoop supergroup 1050 2016-04-19 15:57 /xubo/tianchi/cainiao/file/data/input/config1P.csv/_metadata
-rw-r--r-- 3 hadoop supergroup 20703 2016-04-19 15:57 /xubo/tianchi/cainiao/file/data/input/config1P.csv/part-r-00000-ea5833bd-c663-4709-a2fa-5013f2235c01.gz.parquet
-rw-r--r-- 3 hadoop supergroup 17778 2016-04-19 15:57 /xubo/tianchi/cainiao/file/data/input/config1P.csv/part-r-00001-ea5833bd-c663-4709-a2fa-5013f2235c01.gz.parquet
-rw-r--r-- 3 hadoop supergroup 22612859 2016-04-19 15:31 /xubo/tianchi/cainiao/file/data/input/item_feature1.csv
drwxr-xr-x - hadoop supergroup 0 2016-04-19 15:57 /xubo/tianchi/cainiao/file/data/input/item_feature1P.csv
-rw-r--r-- 3 hadoop supergroup 0 2016-04-19 15:57 /xubo/tianchi/cainiao/file/data/input/item_feature1P.csv/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 346 2016-04-19 15:57 /xubo/tianchi/cainiao/file/data/input/item_feature1P.csv/_common_metadata
-rw-r--r-- 3 hadoop supergroup 1007 2016-04-19 15:57 /xubo/tianchi/cainiao/file/data/input/item_feature1P.csv/_metadata
-rw-r--r-- 3 hadoop supergroup 8054 2016-04-19 15:57 /xubo/tianchi/cainiao/file/data/input/item_feature1P.csv/part-r-00000-5473f84e-cc3d-4191-8227-0108ecee016f.gz.parquet
-rw-r--r-- 3 hadoop supergroup 8640 2016-04-19 15:57 /xubo/tianchi/cainiao/file/data/input/item_feature1P.csv/part-r-00001-5473f84e-cc3d-4191-8227-0108ecee016f.gz.parquet
-rw-r--r-- 3 hadoop supergroup 87835781 2016-04-19 15:31 /xubo/tianchi/cainiao/file/data/input/item_store_feature1.csv
drwxr-xr-x - hadoop supergroup 0 2016-04-19 15:58 /xubo/tianchi/cainiao/file/data/input/item_store_feature1P.csv
-rw-r--r-- 3 hadoop supergroup 0 2016-04-19 15:58 /xubo/tianchi/cainiao/file/data/input/item_store_feature1P.csv/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 346 2016-04-19 15:58 /xubo/tianchi/cainiao/file/data/input/item_store_feature1P.csv/_common_metadata
-rw-r--r-- 3 hadoop supergroup 1007 2016-04-19 15:58 /xubo/tianchi/cainiao/file/data/input/item_store_feature1P.csv/_metadata
-rw-r--r-- 3 hadoop supergroup 8054 2016-04-19 15:58 /xubo/tianchi/cainiao/file/data/input/item_store_feature1P.csv/part-r-00000-796cd827-09b8-41eb-a6dd-4ecac5076957.gz.parquet
-rw-r--r-- 3 hadoop supergroup 8640 2016-04-19 15:58 /xubo/tianchi/cainiao/file/data/input/item_store_feature1P.csv/part-r-00001-796cd827-09b8-41eb-a6dd-4ecac5076957.gz.parquet
-rw-r--r-- 3 hadoop supergroup 64010 2016-04-19 15:31 /xubo/tianchi/cainiao/file/data/input/sample_submission.csv
drwxr-xr-x - hadoop supergroup 0 2016-04-19 15:56 /xubo/tianchi/cainiao/file/data/input/sample_submissionP.csv
-rw-r--r-- 3 hadoop supergroup 0 2016-04-19 15:56 /xubo/tianchi/cainiao/file/data/input/sample_submissionP.csv/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 346 2016-04-19 15:56 /xubo/tianchi/cainiao/file/data/input/sample_submissionP.csv/_common_metadata
-rw-r--r-- 3 hadoop supergroup 1007 2016-04-19 15:56 /xubo/tianchi/cainiao/file/data/input/sample_submissionP.csv/_metadata
-rw-r--r-- 3 hadoop supergroup 8054 2016-04-19 15:56 /xubo/tianchi/cainiao/file/data/input/sample_submissionP.csv/part-r-00000-5a20b4cc-c9b9-4f47-a188-24d801e5e24c.gz.parquet
-rw-r--r-- 3 hadoop supergroup 8640 2016-04-19 15:56 /xubo/tianchi/cainiao/file/data/input/sample_submissionP.csv/part-r-00001-5a20b4cc-c9b9-4f47-a188-24d801e5e24c.gz.parquet
drwxr-xr-x - hadoop supergroup 0 2016-04-19 15:31 /xubo/tianchi/cainiao/file/data/output
drwxr-xr-x - hadoop supergroup 0 2016-04-19 15:31 /xubo/tianchi/cainiao/file/data/output/newcars20160419025203955.csv
-rw-r--r-- 3 hadoop supergroup 0 2016-04-19 15:31 /xubo/tianchi/cainiao/file/data/output/newcars20160419025203955.csv/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 27 2016-04-19 15:31 /xubo/tianchi/cainiao/file/data/output/newcars20160419025203955.csv/part-00000
-rw-r--r-- 3 hadoop supergroup 17832079 2016-04-19 15:31 /xubo/tianchi/cainiao/file.zip
drwx------ - hadoop supergroup 0 2016-03-04 15:48 /xubo/tmp
drwx------ - hadoop supergroup 0 2015-07-23 12:14 /xubo/tmp/hadoop-yarn
drwx------ - hadoop supergroup 0 2015-07-23 12:14 /xubo/tmp/hadoop-yarn/staging
drwx------ - hadoop supergroup 0 2015-07-23 12:14 /xubo/tmp/hadoop-yarn/staging/hadoop
drwx------ - hadoop supergroup 0 2015-09-20 15:48 /xubo/tmp/hadoop-yarn/staging/hadoop/.staging
drwxr-xr-x - hadoop supergroup 0 2015-07-28 20:14 /xubo/tmp/hadoop-yarn/staging/history
drwxrwx--- - hadoop supergroup 0 2015-07-28 20:15 /xubo/tmp/hadoop-yarn/staging/history/done
drwxrwx--- - hadoop supergroup 0 2015-09-20 15:51 /xubo/tmp/hadoop-yarn/staging/history/done/2015
drwxrwx--- - hadoop supergroup 0 2015-07-29 09:18 /xubo/tmp/hadoop-yarn/staging/history/done/2015/07
drwxrwx--- - hadoop supergroup 0 2015-07-30 20:15 /xubo/tmp/hadoop-yarn/staging/history/done/2015/07/23
drwxrwx--- - hadoop supergroup 0 2015-08-01 20:15 /xubo/tmp/hadoop-yarn/staging/history/done/2015/07/24
drwxrwx--- - hadoop supergroup 0 2015-08-04 20:15 /xubo/tmp/hadoop-yarn/staging/history/done/2015/07/28
drwxrwx--- - hadoop supergroup 0 2015-08-05 20:15 /xubo/tmp/hadoop-yarn/staging/history/done/2015/07/29
drwxrwx--- - hadoop supergroup 0 2015-08-10 10:24 /xubo/tmp/hadoop-yarn/staging/history/done/2015/08
drwxrwx--- - hadoop supergroup 0 2015-08-09 20:15 /xubo/tmp/hadoop-yarn/staging/history/done/2015/08/02
drwxrwx--- - hadoop supergroup 0 2015-08-17 20:15 /xubo/tmp/hadoop-yarn/staging/history/done/2015/08/10
drwxrwx--- - hadoop supergroup 0 2015-09-20 15:51 /xubo/tmp/hadoop-yarn/staging/history/done/2015/09
drwxrwx--- - hadoop supergroup 0 2015-09-27 20:15 /xubo/tmp/hadoop-yarn/staging/history/done/2015/09/20
drwxrwxrwt - hadoop supergroup 0 2015-07-23 12:14 /xubo/tmp/hadoop-yarn/staging/history/done_intermediate
drwxrwx--- - hadoop supergroup 0 2015-09-20 15:51 /xubo/tmp/hadoop-yarn/staging/history/done_intermediate/hadoop
drwxr-xr-x - hadoop supergroup 0 2016-02-23 22:46 /xubo/tmp/small128.adam
-rw-r--r-- 3 hadoop supergroup 0 2016-02-23 22:46 /xubo/tmp/small128.adam/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 3444 2016-02-23 22:46 /xubo/tmp/small128.adam/_common_metadata
-rw-r--r-- 3 hadoop supergroup 21284 2016-02-23 22:46 /xubo/tmp/small128.adam/_metadata
-rw-r--r-- 3 hadoop supergroup 35646759 2016-02-23 22:43 /xubo/tmp/small128.adam/part-r-00000.gz.parquet
-rw-r--r-- 3 hadoop supergroup 35617269 2016-02-23 22:43 /xubo/tmp/small128.adam/part-r-00001.gz.parquet
-rw-r--r-- 3 hadoop supergroup 35580901 2016-02-23 22:44 /xubo/tmp/small128.adam/part-r-00002.gz.parquet
-rw-r--r-- 3 hadoop supergroup 35657435 2016-02-23 22:44 /xubo/tmp/small128.adam/part-r-00003.gz.parquet
-rw-r--r-- 3 hadoop supergroup 35587814 2016-02-23 22:45 /xubo/tmp/small128.adam/part-r-00004.gz.parquet
-rw-r--r-- 3 hadoop supergroup 35655298 2016-02-23 22:45 /xubo/tmp/small128.adam/part-r-00005.gz.parquet
-rw-r--r-- 3 hadoop supergroup 35567944 2016-02-23 22:46 /xubo/tmp/small128.adam/part-r-00006.gz.parquet
drwxr-xr-x - hadoop supergroup 0 2016-01-07 17:09 /xubo/tmp/small2.adam
-rw-r--r-- 3 hadoop supergroup 0 2016-01-07 17:09 /xubo/tmp/small2.adam/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 13353 2016-01-07 17:09 /xubo/tmp/small2.adam/_common_metadata
-rw-r--r-- 3 hadoop supergroup 17790 2016-01-07 17:09 /xubo/tmp/small2.adam/_metadata
-rw-r--r-- 3 hadoop supergroup 20462 2016-01-07 17:09 /xubo/tmp/small2.adam/part-r-00000.gz.parquet
drwxr-xr-x - hadoop supergroup 0 2016-02-28 21:18 /xubo/tmp/small228.adam
drwxr-xr-x - hadoop supergroup 0 2016-02-28 21:18 /xubo/tmp/small228.adam/_temporary
drwxr-xr-x - hadoop supergroup 0 2016-02-28 21:18 /xubo/tmp/small228.adam/_temporary/0
drwx------ - hadoop supergroup 0 2015-07-28 20:11 /xubo/tmp/temp-211172541
drwx------ - hadoop supergroup 0 2015-07-28 20:11 /xubo/tmp/temp-211172541/tmp-2072285845
-rw-r--r-- 3 hadoop supergroup 176285 2015-07-28 20:11 /xubo/tmp/temp-211172541/tmp-2072285845/automaton-1.11-8.jar
drwx------ - hadoop supergroup 0 2015-07-28 20:11 /xubo/tmp/temp-211172541/tmp-249311997
-rw-r--r-- 3 hadoop supergroup 164368 2015-07-28 20:11 /xubo/tmp/temp-211172541/tmp-249311997/antlr-runtime-3.4.jar
drwx------ - hadoop supergroup 0 2015-07-28 20:11 /xubo/tmp/temp-211172541/tmp-335058382
-rw-r--r-- 3 hadoop supergroup 4321305 2015-07-28 20:11 /xubo/tmp/temp-211172541/tmp-335058382/pig-0.15.0-core-h2.jar
drwx------ - hadoop supergroup 0 2015-07-28 20:11 /xubo/tmp/temp-211172541/tmp557020053
-rw-r--r-- 3 hadoop supergroup 588001 2015-07-28 20:11 /xubo/tmp/temp-211172541/tmp557020053/joda-time-2.5.jar
drwx------ - hadoop supergroup 0 2015-07-28 20:11 /xubo/tmp/temp1878562490
drwx------ - hadoop supergroup 0 2015-07-28 20:11 /xubo/tmp/temp1878562490/tmp-1043449647
-rw-r--r-- 3 hadoop supergroup 164368 2015-07-28 20:11 /xubo/tmp/temp1878562490/tmp-1043449647/antlr-runtime-3.4.jar
drwxr-xr-x - hadoop supergroup 0 2015-07-28 20:11 /xubo/tmp/temp1878562490/tmp-1606588764
-rw-r--r-- 3 hadoop supergroup 0 2015-07-28 20:11 /xubo/tmp/temp1878562490/tmp-1606588764/_SUCCESS
-rw-r--r-- 3 hadoop supergroup 18 2015-07-28 20:11 /xubo/tmp/temp1878562490/tmp-1606588764/part-m-00000
drwx------ - hadoop supergroup 0 2015-07-28 20:11 /xubo/tmp/temp1878562490/tmp-308674770
-rw-r--r-- 3 hadoop supergroup 176285 2015-07-28 20:11 /xubo/tmp/temp1878562490/tmp-308674770/automaton-1.11-8.jar
drwx------ - hadoop supergroup 0 2015-07-28 20:11 /xubo/tmp/temp1878562490/tmp-362827765
-rw-r--r-- 3 hadoop supergroup 588001 2015-07-28 20:11 /xubo/tmp/temp1878562490/tmp-362827765/joda-time-2.5.jar
drwx------ - hadoop supergroup 0 2015-07-28 20:11 /xubo/tmp/temp1878562490/tmp192938893
-rw-r--r-- 3 hadoop supergroup 4321305 2015-07-28 20:11 /xubo/tmp/temp1878562490/tmp192938893/pig-0.15.0-core-h2.jar
drwx------ - hadoop supergroup 0 2015-07-28 20:09 /xubo/tmp/temp716903836
drwx------ - hadoop supergroup 0 2015-07-28 20:09 /xubo/tmp/temp716903836/tmp-1473902373
-rw-r--r-- 3 hadoop supergroup 176285 2015-07-28 20:09 /xubo/tmp/temp716903836/tmp-1473902373/automaton-1.11-8.jar
drwx------ - hadoop supergroup 0 2015-07-28 20:09 /xubo/tmp/temp716903836/tmp-61781648
-rw-r--r-- 3 hadoop supergroup 588001 2015-07-28 20:09 /xubo/tmp/temp716903836/tmp-61781648/joda-time-2.5.jar
drwx------ - hadoop supergroup 0 2015-07-28 20:09 /xubo/tmp/temp716903836/tmp-886610431
-rw-r--r-- 3 hadoop supergroup 4321305 2015-07-28 20:09 /xubo/tmp/temp716903836/tmp-886610431/pig-0.15.0-core-h2.jar
drwx------ - hadoop supergroup 0 2015-07-28 20:09 /xubo/tmp/temp716903836/tmp1370248212
-rw-r--r-- 3 hadoop supergroup 164368 2015-07-28 20:09 /xubo/tmp/temp716903836/tmp1370248212/antlr-runtime-3.4.jar
hadoop@Master:~/xubo/data/testTools/se$ hadoop fs -ls /xubo/
Found 14 items
drwxr-xr-x - hadoop supergroup 0 2016-04-11 10:50 /xubo/GRCH38Sub
drwxr-xr-x - hadoop supergroup 0 2016-05-13 22:05 /xubo/adam
drwxr-xr-x - hadoop supergroup 0 2016-05-27 22:51 /xubo/avocado
drwxr-xr-x - xubo supergroup 0 2016-03-31 21:51 /xubo/bwa
drwxr-xr-x - hadoop supergroup 0 2016-05-04 15:58 /xubo/data
drwxr-xr-x - xubo supergroup 0 2016-01-26 15:50 /xubo/in1
drwxr-xr-x - xubo supergroup 0 2016-03-28 18:45 /xubo/input
drwxr-xr-x - xubo601450868 supergroup 0 2015-07-26 22:13 /xubo/input726
drwxr-xr-x - hadoop supergroup 0 2016-03-16 10:54 /xubo/log
drwxr-xr-x - hadoop supergroup 0 2016-05-04 15:51 /xubo/output
drwxr-xr-x - hadoop supergroup 0 2016-04-05 09:26 /xubo/sh
drwxr-xr-x - hadoop supergroup 0 2016-04-20 00:34 /xubo/spark
drwxr-xr-x - hadoop supergroup 0 2016-04-19 15:31 /xubo/tianchi
drwx------ - hadoop supergroup 0 2016-03-04 15:48 /xubo/tmp
hadoop@Master:~/xubo/data/testTools/se$ hadoop fs -ls /xubo/GRCH38Sub
Found 18 items
-rw-r--r-- 3 hadoop supergroup 892227087 2016-04-11 10:45 /xubo/GRCH38Sub/GRCH38L12566578.fna
-rw-r--r-- 3 hadoop supergroup 3852 2016-04-11 10:45 /xubo/GRCH38Sub/GRCH38L12566578.fna.amb
-rw-r--r-- 3 hadoop supergroup 552 2016-04-11 10:45 /xubo/GRCH38Sub/GRCH38L12566578.fna.ann
-rw-r--r-- 3 hadoop supergroup 879660156 2016-04-11 10:46 /xubo/GRCH38Sub/GRCH38L12566578.fna.bwt
-rw-r--r-- 3 hadoop supergroup 219915018 2016-04-11 10:47 /xubo/GRCH38Sub/GRCH38L12566578.fna.pac
-rw-r--r-- 3 hadoop supergroup 439830088 2016-04-11 10:47 /xubo/GRCH38Sub/GRCH38L12566578.fna.sa
-rw-r--r-- 3 hadoop supergroup 252513055 2016-04-11 10:48 /xubo/GRCH38Sub/GRCH38chr1L3556522.fna
-rw-r--r-- 3 hadoop supergroup 2527 2016-04-11 10:48 /xubo/GRCH38Sub/GRCH38chr1L3556522.fna.amb
-rw-r--r-- 3 hadoop supergroup 144 2016-04-11 10:48 /xubo/GRCH38Sub/GRCH38chr1L3556522.fna.ann
-rw-r--r-- 3 hadoop supergroup 248956524 2016-04-11 10:48 /xubo/GRCH38Sub/GRCH38chr1L3556522.fna.bwt
-rw-r--r-- 3 hadoop supergroup 62239107 2016-04-11 10:48 /xubo/GRCH38Sub/GRCH38chr1L3556522.fna.pac
-rw-r--r-- 3 hadoop supergroup 124478264 2016-04-11 10:48 /xubo/GRCH38Sub/GRCH38chr1L3556522.fna.sa
-rw-r--r-- 3 hadoop supergroup 498166604 2016-04-11 10:49 /xubo/GRCH38Sub/GRCH38chr1chr2L7016431.fna
-rw-r--r-- 3 hadoop supergroup 3086 2016-04-11 10:49 /xubo/GRCH38Sub/GRCH38chr1chr2L7016431.fna.amb
-rw-r--r-- 3 hadoop supergroup 280 2016-04-11 10:49 /xubo/GRCH38Sub/GRCH38chr1chr2L7016431.fna.ann
-rw-r--r-- 3 hadoop supergroup 491150024 2016-04-11 10:49 /xubo/GRCH38Sub/GRCH38chr1chr2L7016431.fna.bwt
-rw-r--r-- 3 hadoop supergroup 122787489 2016-04-11 10:50 /xubo/GRCH38Sub/GRCH38chr1chr2L7016431.fna.pac
-rw-r--r-- 3 hadoop supergroup 245575024 2016-04-11 10:50 /xubo/GRCH38Sub/GRCH38chr1chr2L7016431.fna.sa
hadoop@Master:~/xubo/data/testTools/se$ hadoop fs -ls /xubo/adam
Found 10 items
drwxr-xr-x - hadoop supergroup 0 2016-03-10 22:24 /xubo/adam/NA12878
-rw-r--r-- 3 hadoop supergroup 255818 2016-03-07 22:09 /xubo/adam/adamAMPLAB
-rw-r--r-- 3 hadoop supergroup 255818 2016-03-07 22:15 /xubo/adam/dataAMPLAB
drwxr-xr-x - hadoop supergroup 0 2016-03-04 16:01 /xubo/adam/dataAdam
-rw-r--r-- 3 hadoop supergroup 24246 2016-03-06 19:10 /xubo/adam/examples
-rw-r--r-- 3 hadoop supergroup 24246 2016-03-06 19:10 /xubo/adam/exampls
drwxr-xr-x - hadoop supergroup 0 2016-04-15 17:06 /xubo/adam/hs38DH
drwxr-xr-x - xubo supergroup 0 2016-04-09 20:31 /xubo/adam/output
drwxr-xr-x - hadoop supergroup 0 2016-05-13 22:51 /xubo/adam/resources
drwxr-xr-x - xubo supergroup 0 2016-03-04 16:01 /xubo/adam/tmp
hadoop@Master:~/xubo/data/testTools/se$ hadoop fs -ls /xubo/adam/dataAdam
Found 58 items
-rw-r--r-- 3 hadoop supergroup 4308 2016-03-04 16:01 /xubo/adam/dataAdam/Hs_Ensembl_example_genes.gtf
-rw-r--r-- 3 hadoop supergroup 1128 2016-03-04 16:01 /xubo/adam/dataAdam/artificial.README.txt
-rw-r--r-- 3 hadoop supergroup 1154 2016-03-04 16:01 /xubo/adam/dataAdam/artificial.fa
-rw-r--r-- 3 hadoop supergroup 3059 2016-03-04 16:01 /xubo/adam/dataAdam/artificial.realigned.sam
-rw-r--r-- 3 hadoop supergroup 2192 2016-03-04 16:01 /xubo/adam/dataAdam/artificial.sam
-rw-r--r-- 3 hadoop supergroup 415380 2016-03-04 16:01 /xubo/adam/dataAdam/bqsr1-ref.observed
-rw-r--r-- 3 hadoop supergroup 381096 2016-03-04 16:01 /xubo/adam/dataAdam/bqsr1.sam
-rw-r--r-- 3 hadoop supergroup 24902 2016-03-04 16:01 /xubo/adam/dataAdam/bqsr1.snps
-rw-r--r-- 3 hadoop supergroup 25412 2016-03-04 16:01 /xubo/adam/dataAdam/bqsr1.vcf
-rw-r--r-- 3 hadoop supergroup 59027 2016-03-04 16:01 /xubo/adam/dataAdam/chr20.250k.fa.gz
-rw-r--r-- 3 hadoop supergroup 186 2016-03-04 16:01 /xubo/adam/dataAdam/dict_with_accession.dict
-rw-r--r-- 3 hadoop supergroup 523 2016-03-04 16:01 /xubo/adam/dataAdam/example_intervals.list
-rw-r--r-- 3 hadoop supergroup 44 2016-03-04 16:01 /xubo/adam/dataAdam/fastq_noqual.fq
-rw-r--r-- 3 hadoop supergroup 3248 2016-03-04 16:01 /xubo/adam/dataAdam/fastq_sample1.fq
-rw-r--r-- 3 hadoop supergroup 3211 2016-03-04 16:01 /xubo/adam/dataAdam/fastq_sample2.fq
-rw-r--r-- 3 hadoop supergroup 2707 2016-03-04 16:01 /xubo/adam/dataAdam/fastq_sample3.fq
-rw-r--r-- 3 hadoop supergroup 2419 2016-03-04 16:01 /xubo/adam/dataAdam/fastq_sample4.fq
-rw-r--r-- 3 hadoop supergroup 2013 2016-03-04 16:01 /xubo/adam/dataAdam/gencode.v19.pc_transcripts.250k.fa.gz
-rw-r--r-- 3 hadoop supergroup 4221 2016-03-04 16:01 /xubo/adam/dataAdam/hg19.chrM.2bit
-rw-r--r-- 3 hadoop supergroup 15031 2016-03-04 16:01 /xubo/adam/dataAdam/human_g1k_v37_chr1_59kb.2bit
-rw-r--r-- 3 hadoop supergroup 60991 2016-03-04 16:01 /xubo/adam/dataAdam/human_g1k_v37_chr1_59kb.fasta
-rw-r--r-- 3 hadoop supergroup 1624 2016-03-04 16:01 /xubo/adam/dataAdam/improper_pairs_1.fq
-rw-r--r-- 3 hadoop supergroup 1084 2016-03-04 16:01 /xubo/adam/dataAdam/improper_pairs_2.fq
-rw-r--r-- 3 hadoop supergroup 3248 2016-03-04 16:01 /xubo/adam/dataAdam/interleaved_fastq_sample1.ifq
-rw-r--r-- 3 hadoop supergroup 3464 2016-03-04 16:01 /xubo/adam/dataAdam/interleaved_fastq_sample1.ifq.output
-rw-r--r-- 3 hadoop supergroup 3211 2016-03-04 16:01 /xubo/adam/dataAdam/interleaved_fastq_sample2.ifq
-rw-r--r-- 3 hadoop supergroup 2310 2016-03-04 16:01 /xubo/adam/dataAdam/interleaved_fastq_sample2.ifq.output
-rw-r--r-- 3 hadoop supergroup 2707 2016-03-04 16:01 /xubo/adam/dataAdam/interleaved_fastq_sample3.ifq
-rw-r--r-- 3 hadoop supergroup 2310 2016-03-04 16:01 /xubo/adam/dataAdam/interleaved_fastq_sample3.ifq.output
-rw-r--r-- 3 hadoop supergroup 2419 2016-03-04 16:01 /xubo/adam/dataAdam/interleaved_fastq_sample4.ifq
-rw-r--r-- 3 hadoop supergroup 2310 2016-03-04 16:01 /xubo/adam/dataAdam/interleaved_fastq_sample4.ifq.output
-rw-r--r-- 3 hadoop supergroup 3256 2016-03-04 16:01 /xubo/adam/dataAdam/multiline_fastq.fq
-rw-r--r-- 3 hadoop supergroup 4511 2016-03-04 16:01 /xubo/adam/dataAdam/ordered.sam
-rw-r--r-- 3 hadoop supergroup 1624 2016-03-04 16:01 /xubo/adam/dataAdam/proper_pairs_1.fq
-rw-r--r-- 3 hadoop supergroup 1624 2016-03-04 16:01 /xubo/adam/dataAdam/proper_pairs_2.fq
-rw-r--r-- 3 hadoop supergroup 23301 2016-03-04 16:01 /xubo/adam/dataAdam/reads-0-2-0
-rw-r--r-- 3 hadoop supergroup 30444 2016-03-04 16:01 /xubo/adam/dataAdam/reads12.sam
-rw-r--r-- 3 hadoop supergroup 30444 2016-03-04 16:01 /xubo/adam/dataAdam/reads12_diff1.sam
-rw-r--r-- 3 hadoop supergroup 30446 2016-03-04 16:01 /xubo/adam/dataAdam/reads21.sam
drwxr-xr-x - hadoop supergroup 0 2016-03-04 16:01 /xubo/adam/dataAdam/resources
-rw-r--r-- 3 hadoop supergroup 3536 2016-03-04 16:01 /xubo/adam/dataAdam/single_fastq_sample1.fq.output
-rw-r--r-- 3 hadoop supergroup 2947 2016-03-04 16:01 /xubo/adam/dataAdam/single_fastq_sample2.fq.output
-rw-r--r-- 3 hadoop supergroup 2947 2016-03-04 16:01 /xubo/adam/dataAdam/single_fastq_sample3.fq.output
-rw-r--r-- 3 hadoop supergroup 2358 2016-03-04 16:01 /xubo/adam/dataAdam/single_fastq_sample4.fq.output
-rw-r--r-- 3 hadoop supergroup 3093 2016-03-04 16:01 /xubo/adam/dataAdam/small.sam
-rw-r--r-- 3 hadoop supergroup 15651 2016-03-04 16:01 /xubo/adam/dataAdam/small.vcf
-rw-r--r-- 3 hadoop supergroup 15627 2016-03-04 16:01 /xubo/adam/dataAdam/small_missing.vcf
-rw-r--r-- 3 hadoop supergroup 70 2016-03-04 16:01 /xubo/adam/dataAdam/small_realignment_targets.intervals
-rw-r--r-- 3 hadoop supergroup 30296 2016-03-04 16:01 /xubo/adam/dataAdam/small_realignment_targets.pileup
-rw-r--r-- 3 hadoop supergroup 2759 2016-03-04 16:01 /xubo/adam/dataAdam/small_realignment_targets.sam
-rw-r--r-- 3 hadoop supergroup 2090 2016-03-04 16:01 /xubo/adam/dataAdam/small_realignment_targets_README.txt
-rw-r--r-- 3 hadoop supergroup 327 2016-03-04 16:01 /xubo/adam/dataAdam/sorted.sam
-rw-r--r-- 3 hadoop supergroup 718 2016-03-04 16:01 /xubo/adam/dataAdam/tags.sam
-rw-r--r-- 3 hadoop supergroup 96 2016-03-04 16:01 /xubo/adam/dataAdam/test.conf
-rw-r--r-- 3 hadoop supergroup 59 2016-03-04 16:01 /xubo/adam/dataAdam/test_rowgroup_rangeindex.1.txt
-rw-r--r-- 3 hadoop supergroup 29408 2016-03-04 16:01 /xubo/adam/dataAdam/unmapped.sam
-rw-r--r-- 3 hadoop supergroup 4511 2016-03-04 16:01 /xubo/adam/dataAdam/unordered.sam
-rw-r--r-- 3 hadoop supergroup 327 2016-03-04 16:01 /xubo/adam/dataAdam/unsorted.sam
hadoop@Master:~/xubo/data/testTools/se$
hadoop@Master:~/xubo/data/testTools/se$ ls
60IrX9dA.jar hs1.bam hs1.sai hs1.snp.vcf hs1.sorted.bam.bcf hs2.bcf hs2.sai hs2.sort.bam OJuVwLJQ.jar RqS4b2ZW.jar T7sFxfyV.jar
avocado hs1.fq hs1.sam hs1.sorted.bam hs2.bam hs2.fq hs2.sam hs2.vcf QxOhexoz.jar snap-basic.properties Zy2ksUUd.jar
hadoop@Master:~/xubo/data/testTools/se$ pwd
/home/hadoop/xubo/data/testTools/se
hadoop@Master:~/xubo/data/testTools/se$ avocado-submit /xubo/avocado/hs2.fq /xubo/avocado/hs38DH.fa /xubo/avocado/test20160527NUMhs2snap /home/hadoop/xubo/data/testTools/se/snap-basic.properties
Using SPARK_SUBMIT=/home/hadoop/cloud/spark-1.5.2//bin/spark-submit
Command body threw exception:
java.lang.IllegalArgumentException: No input stage with name: SnapInputStage
Exception in thread "main" java.lang.IllegalArgumentException: No input stage with name: SnapInputStage
at org.bdgenomics.avocado.input.Input$.apply(Input.scala:57)
at org.bdgenomics.avocado.cli.Avocado$$anonfun$4.apply(Avocado.scala:208)
at org.bdgenomics.avocado.cli.Avocado$$anonfun$4.apply(Avocado.scala:208)
at org.apache.spark.rdd.Timer.time(Timer.scala:57)
at org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:207)
at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:54)
at org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:82)
at org.bdgenomics.utils.cli.BDGCommandCompanion$class.main(BDGCommand.scala:32)
at org.bdgenomics.avocado.cli.Avocado$.main(Avocado.scala:52)
at org.bdgenomics.avocado.cli.Avocado.main(Avocado.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:674)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
hadoop@Master:~/xubo/data/testTools/se$ vi snap-basic.properties
hadoop@Master:~/xubo/data/testTools/se$ vi snap-basic.properties
hadoop@Master:~/xubo/data/testTools/se$ avocado-submit /xubo/avocado/hs2.fq /xubo/avocado/hs38DH.fa /xubo/avocado/test20160527NUMhs2snap /home/hadoop/xubo/data/testTools/se/snap-basic.properties
Using SPARK_SUBMIT=/home/hadoop/cloud/spark-1.5.2//bin/spark-submit
Command body threw exception:
java.lang.IllegalArgumentException: Passed in key must select exactly one node: AlignedReads
Exception in thread "main" java.lang.IllegalArgumentException: Passed in key must select exactly one node: AlignedReads
at org.apache.commons.configuration.HierarchicalConfiguration.configurationAt(HierarchicalConfiguration.java:576)
at org.apache.commons.configuration.HierarchicalConfiguration.configurationAt(HierarchicalConfiguration.java:596)
at org.bdgenomics.avocado.input.Input$.apply(Input.scala:52)
at org.bdgenomics.avocado.cli.Avocado$$anonfun$4.apply(Avocado.scala:208)
at org.bdgenomics.avocado.cli.Avocado$$anonfun$4.apply(Avocado.scala:208)
at org.apache.spark.rdd.Timer.time(Timer.scala:57)
at org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:207)
at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:54)
at org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:82)
at org.bdgenomics.utils.cli.BDGCommandCompanion$class.main(BDGCommand.scala:32)
at org.bdgenomics.avocado.cli.Avocado$.main(Avocado.scala:52)
at org.bdgenomics.avocado.cli.Avocado.main(Avocado.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:674)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
hadoop@Master:~/xubo/data/testTools/se$ vi snap-basic.properties
hadoop@Master:~/xubo/data/testTools/se$ avocado-submit /xubo/avocado/hs2.fq /xubo/avocado/hs38DH.fa /xubo/avocado/test20160527NUMhs2snap /home/hadoop/xubo/data/testTools/se/snap-basic.properties
Using SPARK_SUBMIT=/home/hadoop/cloud/spark-1.5.2//bin/spark-submit
Command body threw exception:
java.lang.IllegalArgumentException: No input stage with name: /xubo/avocado/
Exception in thread "main" java.lang.IllegalArgumentException: No input stage with name: /xubo/avocado/
at org.bdgenomics.avocado.input.Input$.apply(Input.scala:57)
at org.bdgenomics.avocado.cli.Avocado$$anonfun$4.apply(Avocado.scala:208)
at org.bdgenomics.avocado.cli.Avocado$$anonfun$4.apply(Avocado.scala:208)
at org.apache.spark.rdd.Timer.time(Timer.scala:57)
at org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:207)
at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:54)
at org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:82)
at org.bdgenomics.utils.cli.BDGCommandCompanion$class.main(BDGCommand.scala:32)
at org.bdgenomics.avocado.cli.Avocado$.main(Avocado.scala:52)
at org.bdgenomics.avocado.cli.Avocado.main(Avocado.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:674)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
hadoop@Master:~/xubo/data/testTools/se$ vi snap-basic.properties
hadoop@Master:~/xubo/data/testTools/se$ avocado-submit /xubo/avocado/hs2.fq /xubo/avocado/hs38DH.fa /xubo/avocado/test20160527NUMhs2snap /home/hadoop/xubo/data/testTools/se/snap-basic.properties
Using SPARK_SUBMIT=/home/hadoop/cloud/spark-1.5.2//bin/spark-submit
Command body threw exception:
java.lang.IllegalArgumentException: No input stage with name: /xubo/avocado/hs2.fq
Exception in thread "main" java.lang.IllegalArgumentException: No input stage with name: /xubo/avocado/hs2.fq
at org.bdgenomics.avocado.input.Input$.apply(Input.scala:57)
at org.bdgenomics.avocado.cli.Avocado$$anonfun$4.apply(Avocado.scala:208)
at org.bdgenomics.avocado.cli.Avocado$$anonfun$4.apply(Avocado.scala:208)
at org.apache.spark.rdd.Timer.time(Timer.scala:57)
at org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:207)
at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:54)
at org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:82)
at org.bdgenomics.utils.cli.BDGCommandCompanion$class.main(BDGCommand.scala:32)
at org.bdgenomics.avocado.cli.Avocado$.main(Avocado.scala:52)
at org.bdgenomics.avocado.cli.Avocado.main(Avocado.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:674)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
hadoop@Master:~/xubo/data/testTools/se$ ls
4DBVKTZu.jar avocado hs1.bam hs1.sai hs1.snp.vcf hs1.sorted.bam.bcf hs2.bcf hs2.sai hs2.sort.bam krppqTxa.jar QxOhexoz.jar snap-basic.properties wrbct4hS.jar
60IrX9dA.jar GqzY8iVY.jar hs1.fq hs1.sam hs1.sorted.bam hs2.bam hs2.fq hs2.sam hs2.vcf OJuVwLJQ.jar RqS4b2ZW.jar T7sFxfyV.jar Zy2ksUUd.jar
hadoop@Master:~/xubo/data/testTools/se$ pwd
/home/hadoop/xubo/data/testTools/se
hadoop@Master:~/xubo/data/testTools/se$ avocado-submit /xubo/avocado/hs2.fq /xubo/avocado/hs38DH.fa /xubo/avocado/test20160527NUMhs2snap /home/hadoop/xubo/data/testTools/se/snap-basic.properties
Using SPARK_SUBMIT=/home/hadoop/cloud/spark-1.5.2//bin/spark-submit
hadoop@Master:~/xubo/data/testTools/se$ vi snap-basic.properties
hadoop@Master:~/xubo/data/testTools/se$ avocado-submit /xubo/avocado/hs2.fq /xubo/avocado/hs38DH.fa /xubo/avocado/test20160527NUMhs2snap /home/hadoop/xubo/data/testTools/se/snap-basic.properties
Using SPARK_SUBMIT=/home/hadoop/cloud/spark-1.5.2//bin/spark-submit
Command body threw exception:
java.lang.IllegalArgumentException: No input stage with name: /home/hadoop/xubo/data/testTools/se/hs2.fq
Exception in thread "main" java.lang.IllegalArgumentException: No input stage with name: /home/hadoop/xubo/data/testTools/se/hs2.fq
at org.bdgenomics.avocado.input.Input$.apply(Input.scala:57)
at org.bdgenomics.avocado.cli.Avocado$$anonfun$4.apply(Avocado.scala:208)
at org.bdgenomics.avocado.cli.Avocado$$anonfun$4.apply(Avocado.scala:208)
at org.apache.spark.rdd.Timer.time(Timer.scala:57)
at org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:207)
at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:54)
at org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:82)
at org.bdgenomics.utils.cli.BDGCommandCompanion$class.main(BDGCommand.scala:32)
at org.bdgenomics.avocado.cli.Avocado$.main(Avocado.scala:52)
at org.bdgenomics.avocado.cli.Avocado.main(Avocado.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:674)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
hadoop@Master:~/xubo/data/testTools/se$ vi snap-basic.properties
{
SnapInputStage =
{
indexDirectory = /Users/fnothaft/IdeaProjects/avocado2/avocado/chrM
snapPath = /Users/fnothaft/IdeaProjects/snap/snap
numMachines = 1
coresPerMachine = 4
}
readExplorer =
{
}
biallelicGenotyper = {
}
defPart =
{
}
#inputStage = SnapInputStage
inputStage = /home/hadoop/xubo/data/testTools/se/hs2.fq
preprocessorNames = ( );
preprocessorAlgorithms = ( );
explorerName = readExplorer;
explorerAlgorithm = ReadExplorer;
genotyperName = biallelicGenotyper;
genotyperAlgorithm = BiallelicGenotyper;
postprocessorNames = ( );
postprocessorAlgorithms = ( );
}
"snap-basic.properties" 32L,640C 1,1 All
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