SMaSH installation error

Question

[pinn]

HI Any one can help me with the SMaSH installation were it went wrong.

[DEBUG] Output directory: /home/likithreddy/Downloads/smash-master/calldiff/target/classes
[DEBUG] CompilerReuseStrategy: reuseCreated
[DEBUG] useIncrementalCompilation enabled
[DEBUG] Stale source detected: /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/CandidateCalls.java
[DEBUG] Stale source detected: /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/BimonotonicAStarSearcher.java
[DEBUG] Stale source detected: /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/OutputTuple.java
[DEBUG] Stale source detected: /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/CommandLine.java
[DEBUG] Stale source detected: /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/ApiCallScanner.java
[DEBUG] Stale source detected: /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/Window.java
[DEBUG] Stale source detected: /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/DiffStats.java
[DEBUG] Stale source detected: /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/Main.java
[INFO] Changes detected - recompiling the module!
[DEBUG] Classpath:
[DEBUG]  /home/likithreddy/Downloads/smash-master/calldiff/target/classes
[DEBUG]  /home/likithreddy/.m2/repository/com/google/guava/guava/17.0/guava-17.0.jar
[DEBUG]  /home/likithreddy/.m2/repository/com/beust/jcommander/1.35/jcommander-1.35.jar
[DEBUG]  /home/likithreddy/.m2/repository/com/google/apis/google-api-services-genomics/v1beta2-rev12-1.19.0/google-api-services-genomics-v1beta2-rev12-1.19.0.jar
[DEBUG]  /home/likithreddy/.m2/repository/com/google/api-client/google-api-client/1.18.0-rc/google-api-client-1.18.0-rc.jar
[DEBUG]  /home/likithreddy/.m2/repository/com/google/oauth-client/google-oauth-client/1.18.0-rc/google-oauth-client-1.18.0-rc.jar
[DEBUG]  /home/likithreddy/.m2/repository/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar
[DEBUG]  /home/likithreddy/.m2/repository/com/google/http-client/google-http-client-jackson2/1.18.0-rc/google-http-client-jackson2-1.18.0-rc.jar
[DEBUG]  /home/likithreddy/.m2/repository/com/google/http-client/google-http-client/1.18.0-rc/google-http-client-1.18.0-rc.jar
[DEBUG]  /home/likithreddy/.m2/repository/org/apache/httpcomponents/httpclient/4.0.1/httpclient-4.0.1.jar
[DEBUG]  /home/likithreddy/.m2/repository/org/apache/httpcomponents/httpcore/4.0.1/httpcore-4.0.1.jar
[DEBUG]  /home/likithreddy/.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar
[DEBUG]  /home/likithreddy/.m2/repository/commons-codec/commons-codec/1.3/commons-codec-1.3.jar
[DEBUG]  /home/likithreddy/.m2/repository/com/fasterxml/jackson/core/jackson-core/2.1.3/jackson-core-2.1.3.jar
[DEBUG]  /home/likithreddy/.m2/repository/com/google/oauth-client/google-oauth-client-java6/1.18.0-rc/google-oauth-client-java6-1.18.0-rc.jar
[DEBUG]  /home/likithreddy/.m2/repository/com/google/oauth-client/google-oauth-client-jetty/1.18.0-rc/google-oauth-client-jetty-1.18.0-rc.jar
[DEBUG]  /home/likithreddy/.m2/repository/org/mortbay/jetty/jetty/6.1.26/jetty-6.1.26.jar
[DEBUG]  /home/likithreddy/.m2/repository/org/mortbay/jetty/jetty-util/6.1.26/jetty-util-6.1.26.jar
[DEBUG]  /home/likithreddy/.m2/repository/org/mortbay/jetty/servlet-api/2.5-20081211/servlet-api-2.5-20081211.jar
[DEBUG]  /home/likithreddy/.m2/repository/com/google/cloud/genomics/google-genomics-utils/v1beta2-0.19/google-genomics-utils-v1beta2-0.19.jar
[DEBUG]  /home/likithreddy/.m2/repository/com/google/api-client/google-api-client-java6/1.19.0/google-api-client-java6-1.19.0.jar
[DEBUG] Source roots:
[DEBUG]  /home/likithreddy/Downloads/smash-master/calldiff/src/main/java
[DEBUG] Command line options:
[DEBUG] -d /home/likithreddy/Downloads/smash-master/calldiff/target/classes -classpath /home/likithreddy/Downloads/smash-master/calldiff/target/classes:/home/likithreddy/.m2/repository/com/google/guava/guava/17.0/guava-17.0.jar:/home/likithreddy/.m2/repository/com/beust/jcommander/1.35/jcommander-1.35.jar:/home/likithreddy/.m2/repository/com/google/apis/google-api-services-genomics/v1beta2-rev12-1.19.0/google-api-services-genomics-v1beta2-rev12-1.19.0.jar:/home/likithreddy/.m2/repository/com/google/api-client/google-api-client/1.18.0-rc/google-api-client-1.18.0-rc.jar:/home/likithreddy/.m2/repository/com/google/oauth-client/google-oauth-client/1.18.0-rc/google-oauth-client-1.18.0-rc.jar:/home/likithreddy/.m2/repository/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar:/home/likithreddy/.m2/repository/com/google/http-client/google-http-client-jackson2/1.18.0-rc/google-http-client-jackson2-1.18.0-rc.jar:/home/likithreddy/.m2/repository/com/google/http-client/google-http-client/1.18.0-rc/google-http-client-1.18.0-rc.jar:/home/likithreddy/.m2/repository/org/apache/httpcomponents/httpclient/4.0.1/httpclient-4.0.1.jar:/home/likithreddy/.m2/repository/org/apache/httpcomponents/httpcore/4.0.1/httpcore-4.0.1.jar:/home/likithreddy/.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar:/home/likithreddy/.m2/repository/commons-codec/commons-codec/1.3/commons-codec-1.3.jar:/home/likithreddy/.m2/repository/com/fasterxml/jackson/core/jackson-core/2.1.3/jackson-core-2.1.3.jar:/home/likithreddy/.m2/repository/com/google/oauth-client/google-oauth-client-java6/1.18.0-rc/google-oauth-client-java6-1.18.0-rc.jar:/home/likithreddy/.m2/repository/com/google/oauth-client/google-oauth-client-jetty/1.18.0-rc/google-oauth-client-jetty-1.18.0-rc.jar:/home/likithreddy/.m2/repository/org/mortbay/jetty/jetty/6.1.26/jetty-6.1.26.jar:/home/likithreddy/.m2/repository/org/mortbay/jetty/jetty-util/6.1.26/jetty-util-6.1.26.jar:/home/likithreddy/.m2/repository/org/mortbay/jetty/servlet-api/2.5-20081211/servlet-api-2.5-20081211.jar:/home/likithreddy/.m2/repository/com/google/cloud/genomics/google-genomics-utils/v1beta2-0.19/google-genomics-utils-v1beta2-0.19.jar:/home/likithreddy/.m2/repository/com/google/api-client/google-api-client-java6/1.19.0/google-api-client-java6-1.19.0.jar: -sourcepath /home/likithreddy/Downloads/smash-master/calldiff/src/main/java: -s /home/likithreddy/Downloads/smash-master/calldiff/target/generated-sources/annotations -g -nowarn -target 1.8 -source 1.8 -encoding UTF-8
[DEBUG] incrementalBuildHelper#beforeRebuildExecution
[INFO] Compiling 19 source files to /home/likithreddy/Downloads/smash-master/calldiff/target/classes
[DEBUG] incrementalBuildHelper#afterRebuildExecution
[INFO] -------------------------------------------------------------
[WARNING] COMPILATION WARNING : 
[INFO] -------------------------------------------------------------
[WARNING] /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/Main.java: /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/Main.java uses or overrides a deprecated API.
[WARNING] /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/Main.java: Recompile with -Xlint:deprecation for details.
[WARNING] Some messages have been simplified; recompile with -Xdiags:verbose to get full output
[INFO] 3 warnings 
[INFO] -------------------------------------------------------------
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/Main.java:[135,21] reference to println is ambiguous
  both method println(char[]) in java.io.PrintStream and method println(java.lang.String) in java.io.PrintStream match
[ERROR] /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/Main.java:[136,20] incompatible types: inferred type does not conform to upper bound(s)
    inferred: edu.berkeley.cs.amplab.calldiff.DiffStats
    upper bound(s): char[],java.lang.Object
[INFO] 2 errors 
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.377 s
[INFO] Finished at: 2018-01-25T18:20:59+05:30
[INFO] Final Memory: 17M/298M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project calldiff: Compilation failure: Compilation failure:
[ERROR] /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/Main.java:[135,21] reference to println is ambiguous
[ERROR] both method println(char[]) in java.io.PrintStream and method println(java.lang.String) in java.io.PrintStream match
[ERROR] /home/likithreddy/Downloads/smash-master/calldiff/src/main/java/edu/berkeley/cs/amplab/calldiff/Main.java:[136,20] incompatible types: inferred type does not conform to upper bound(s)
[ERROR] inferred: edu.berkeley.cs.amplab.calldiff.DiffStats
[ERROR] upper bound(s): char[],java.lang.Object
[ERROR] -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project calldiff: Compilation failure
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:212)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
    at org.apache.maven.lifecycle.internal.MojoExecutor.executeForkedExecutions(MojoExecutor.java:352)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:197)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
    at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
    at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
    at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
    at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
    at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.compiler.CompilationFailureException: Compilation failure
    at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:858)
    at org.apache.maven.plugin.compiler.CompilerMojo.execute(CompilerMojo.java:129)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
    ... 24 more
[ERROR] 
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

[Ram]

Hello pinninti1991reddy!

Please follow up on your questions. See C: Readgroups for a bam file ?

For this reason we have closed your question.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

[Ram]

I'm reopening the question as user has provided feedback.

[GenoMax]

Did you get the source code from here which has the following note:

The Java version of SMaSH is not yet officially supported and should be considered experimental.

[pinn]

yes,https://github.com/amplab/smash, whats the problem with the installation ?

Answer 1

[Len Trigg]

Isn't SMaSH basically abandoned? You may be better to use the benchmarking tools developed by GA4GH which are now widely used, see https://github.com/ga4gh/benchmarking-tools

[pinn]

Thanks for your answer.