search

miso-lims / runscanner

Monitors directories on the file system containing the output from sequencing instruments (e.g. Illumina) and reports their status and metrics
https://miso-lims.github.io/runscanner/
GNU General Public License v3.0
2 stars 1 forks source link

NextSeq 2000: "startDate" : null #147

Closed sklages closed 1 year ago

sklages commented 1 year ago

For NextSeq2000 device it seems that runscanner is not able to read startDate, e.g.:

{
  "platform" : "Illumina",
  "runAlias" : "230113_SN435_5_AACJ7GTM5",
  "sequencerFolderPath" : "/path/to/230113_SN435_5_AACJ7GTM5",
  "sequencerName" : "VH00435",
  "sequencerPosition" : null,
  "containerSerialNumber" : "AACJ7GTM5",
  "containerModel" : null,
  "sequencingKit" : null,
  "laneCount" : 1,
  "healthType" : "COMPLETED",
  "startDate" : null,
  "completionDate" : "2023-01-14T03:19:39.064437Z",
  "pairedEndRun" : false,
  "software" : "Interop: v1.2.0 Instrument: 0",
  "metrics" : "[<...>]" ,
  "bclCount" : 132,
  "callCycle" : 109,
  "chemistry" : "UNKNOWN",
  "imgCycle" : 109,
  "indexLengths" : [ 8 ],
  "numCycles" : 109,
  "numReads" : 1,
  "readLength" : 101,
  "readLengths" : [ 101 ],
  "runBasesMask" : "y101,I8",
  "scoreCycle" : 109,
  "workflowType" : null,
  "indexSequencing" : null
}

Where is the start date usually read/deduced from?

djcooke commented 1 year ago

We are currently working on NextSeq 2000 support, so this should be fixed in the next release

djcooke commented 1 year ago

Release 1.15.0 fixes most of the NextSeq 2000 issues, but it's not detecting the index sequencing correctly (normal vs. i5 reverse compliment). We'll have a fix and patch release to address that soon - likely tomorrow.

djcooke commented 1 year ago

Version 1.15.1 is out, and the output looks all good for the couple of NextSeq 2000 runs we have so far.

No updates to MISO are necessary - this is compatible with any version of MISO that was working with Run Scanner 1.13.3 or later (and likely some older versions)

sklages commented 1 year ago

Thanks for that.

Building v1.15.1 failed here:

-- JsonCpp Version: 1.9.4
<..>
Apache Maven 3.5.2 (138edd61fd100ec658bfa2d307c43b76940a5d7d; 2017-10-18T09:58:13+02:00)
Maven home: /project/miso/current/build_tools/maven/current
Java version: 11.0.13, vendor: Oracle Corporation
Java home: /project/miso/2018/build_tools/jdk/jdk-11.0.13
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "5.15.77.mx64.440", arch: "amd64", family: "unix"
<..>
[WARNING]
[WARNING] Some problems were encountered while building the effective model for ca.on.oicr.gsi.runscanner:runscanner-dto:jar:1.15.1
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ ca.on.oicr.gsi.runscanner:runscanner-dto:[unknown-version], /scratch/local2/miso-runscanner/build/runscanner/dto/pom.xml, line 40, column 15
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
<..>
[WARNING] File encoding has not been set, using platform encoding UTF-8, i.e. build is platform dependent!
[DEBUG] incrementalBuildHelper#beforeRebuildExecution
[INFO] Compiling 10 source files to /scratch/local2/miso-runscanner/build/runscanner/dto/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Run Scanner ........................................ SUCCESS [  0.863 s]
[INFO] runscanner-dto ..................................... FAILURE [  0.702 s]
[INFO] scanner ............................................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.718 s
[INFO] Finished at: 2023-01-25T08:51:19+01:00
[INFO] Final Memory: 16M/96M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project runscanner-dto: Fatal error compiling: error: release version 17 not supported -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project runscanner-dto: Fatal error compiling
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:213)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:154)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:146)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    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:309)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:194)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:107)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:955)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:290)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:194)
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke (Method.java:566)
    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.MojoExecutionException: Fatal error compiling
    at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute (AbstractCompilerMojo.java:1145)
    at org.apache.maven.plugin.compiler.CompilerMojo.execute (CompilerMojo.java:187)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:134)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:208)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:154)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:146)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    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:309)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:194)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:107)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:955)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:290)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:194)
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke (Method.java:566)
    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.codehaus.plexus.compiler.CompilerException: error: release version 17 not supported
    at org.codehaus.plexus.compiler.javac.JavaxToolsCompiler.compileInProcess (JavaxToolsCompiler.java:173)
    at org.codehaus.plexus.compiler.javac.JavacCompiler.performCompile (JavacCompiler.java:174)
    at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute (AbstractCompilerMojo.java:1134)
    at org.apache.maven.plugin.compiler.CompilerMojo.execute (CompilerMojo.java:187)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:134)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:208)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:154)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:146)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    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:309)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:194)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:107)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:955)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:290)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:194)
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke (Method.java:566)
    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: java.lang.IllegalArgumentException: error: release version 17 not supported
    at com.sun.tools.javac.main.Arguments.reportDiag (Arguments.java:891)
    at com.sun.tools.javac.main.Arguments.handleReleaseOptions (Arguments.java:311)
    at com.sun.tools.javac.main.Arguments.processArgs (Arguments.java:350)
    at com.sun.tools.javac.main.Arguments.init (Arguments.java:246)
    at com.sun.tools.javac.api.JavacTool.getTask (JavacTool.java:185)
    at com.sun.tools.javac.api.JavacTool.getTask (JavacTool.java:119)
    at com.sun.tools.javac.api.JavacTool.getTask (JavacTool.java:68)
    at org.codehaus.plexus.compiler.javac.JavaxToolsCompiler.compileInProcess (JavaxToolsCompiler.java:125)
    at org.codehaus.plexus.compiler.javac.JavacCompiler.performCompile (JavacCompiler.java:174)
    at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute (AbstractCompilerMojo.java:1134)
    at org.apache.maven.plugin.compiler.CompilerMojo.execute (CompilerMojo.java:187)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:134)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:208)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:154)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:146)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    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:309)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:194)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:107)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:955)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:290)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:194)
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke (Method.java:566)
    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)
[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/MojoExecutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :runscanner-dto

Any idea what I am missing here?

djcooke commented 1 year ago

Starting with 1.14.0, Run Scanner is now on Java 17, so you'll need to update your JDK used both for building and for Tomcat