Commit a9ea63e5 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding more logging

parent 5c4cadf5
......@@ -69,10 +69,14 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
outputDir = outputDir.getAbsoluteFile
init()
biopetScript()
logger.info("Biopet script done")
if (disableScatter) for (function <- functions) function match {
case f: ScatterGatherableFunction => f.scatterCount = 1
case _ =>
if (disableScatter) {
logger.info("Disable scatters")
for (function <- functions) function match {
case f: ScatterGatherableFunction => f.scatterCount = 1
case _ =>
}
}
this match {
......@@ -81,6 +85,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
case _ => reportClass.foreach(add(_))
}
logger.info("Running pre commands")
for (function <- functions) function match {
case f: BiopetCommandLineFunction =>
f.preProcessExecutable()
......@@ -94,7 +99,8 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, output directory cannot be created")
inputFiles.foreach { i =>
logger.info("Checking input files")
inputFiles.par.foreach { i =>
if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}")
if (!i.file.canRead) Logging.addError(s"Input file can not be read: ${i.file}")
if (!i.file.isAbsolute) Logging.addError(s"Input file should be an absolute path: ${i.file}")
......@@ -111,6 +117,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
if (logger.isDebugEnabled) WriteDependencies.writeDependencies(functions, new File(outputDir, s".log/${qSettings.runName}.deps.json"))
Logging.checkErrors()
logger.info("Script complete without errors")
}
/** Get implemented from org.broadinstitute.gatk.queue.QScript */
......
......@@ -39,6 +39,7 @@ object Logging {
def addError(error: String, debug: String = null): Unit = {
val msg = error + (if (debug != null && logger.isDebugEnabled) "; " + debug else "")
logger.error(msg)
errors.append(new Exception(msg))
}
......
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