基因数据处理68之avocado的配置文件默认无法从hdfs读取

（1）配置文件设置为hdfs路劲有问题

val configFile = "hdfs://219.219.220.149:9000/xubo/avocado/avocado-sample-configs/basic.properties"

报错：

hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem/BWAMEMSparkAll/test$ ./GcdssCallVariant2.sh start:fqFile:hdfs://219.219.220.149:9000/xubo/avocado/artificial/artificial.realigned.samfaFile:hdfs://219.219.220.149:9000/xubo/avocado/artificial/artificial.faconfigFile:hdfs://219.219.220.149:9000/xubo/avocado/avocado-sample-configs/basic.propertiesoutput:hdfs://219.219.220.149:9000/xubo/avocado/test201605281620AvocadoZidai060505fqLoad.count:10faLoad.count:1faLoad:hdfs://219.219.220.149:9000/xubo/avocado/test201605281620AvocadoZidai060505tempPath:/tmp/config8081833845300900496tempFilePath:/tmp/config8081833845300900496/temp.propertiesException in thread "main" org.apache.commons.configuration.ConfigurationException: Cannot locate configuration source hdfs://219.219.220.149:9000/xubo/avocado/avocado-sample-configs/basic.propertiesat org.apache.commons.configuration.AbstractFileConfiguration.load(AbstractFileConfiguration.java:217)at org.apache.commons.configuration.AbstractFileConfiguration.load(AbstractFileConfiguration.java:197)at org.apache.commons.configuration.AbstractHierarchicalFileConfiguration.load(AbstractHierarchicalFileConfiguration.java:164)at org.apache.commons.configuration.AbstractHierarchicalFileConfiguration.<init>(AbstractHierarchicalFileConfiguration.java:91)at org.apache.commons.configuration.plist.PropertyListConfiguration.<init>(PropertyListConfiguration.java:159)at org.gcdss.cli.Gcdss.<init>(Gcdss.scala:84)at org.gcdss.cli.Gcdss$.apply(Gcdss.scala:46)at org.gcdss.cli.GcdssCallVariant$.main(GcdssCallVariant.scala:64)at org.gcdss.cli.GcdssCallVariant.main(GcdssCallVariant.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)

（2）将配置文件设置为本地路劲可以通过：

val configFile = "/home/hadoop/xubo/data/testTools/basic.properties"

记录：

hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem/BWAMEMSparkAll/test$ ./GcdssCallVariant2.sh start:fqFile:hdfs://219.219.220.149:9000/xubo/avocado/artificial/artificial.realigned.samfaFile:hdfs://219.219.220.149:9000/xubo/avocado/artificial/artificial.faconfigFile:/home/hadoop/xubo/data/testTools/basic.propertiesoutput:hdfs://219.219.220.149:9000/xubo/avocado/test201605281620AvocadoZidai060505fqLoad.count:10faLoad.count:1faLoad:hdfs://219.219.220.149:9000/xubo/avocado/test201605281620AvocadoZidai060505tempPath:/tmp/config5809810828492689651tempFilePath:/tmp/config5809810828492689651/temp.propertiesLoading reads in from hdfs://219.219.220.149:9000/xubo/avocado/artificial/artificial.realigned.samSLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".                SLF4J: Defaulting to no-operation (NOP) logger implementationSLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.read parquet:                                                                   *************end*************   

参考

【1】https://github.com/xubo245/AdamLearning【2】https://github.com/bigdatagenomics/adam/ 【3】https://github.com/xubo245/SparkLearning【4】http://spark.apache.org【5】http://stackoverflow.com/questions/28166667/how-to-pass-d-parameter-or-environment-variable-to-spark-job  【6】http://stackoverflow.com/questions/28840438/how-to-override-sparks-log4j-properties-per-driver

研究成果：

【1】 [BIBM] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Chao Wang, and Xuehai Zhou, "Distributed Gene Clinical Decision Support System Based on Cloud Computing", in IEEE International Conference on Bioinformatics and Biomedicine. (BIBM 2017, CCF B)【2】 [IEEE CLOUD] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Xuehai Zhou. Efficient Distributed Smith-Waterman Algorithm Based on Apache Spark (CLOUD 2017, CCF-C).【3】 [CCGrid] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Jinhong Zhou, Xuehai Zhou. DSA: Scalable Distributed Sequence Alignment System Using SIMD Instructions. (CCGrid 2017, CCF-C).【4】more: https://github.com/xubo245/Publications

Help

If you have any questions or suggestions, please write it in the issue of this project or send an e-mail to me: [e-mail]: xu601450868QQ: 601450868