@Override
public ExecutionResult execute(ExecutionContext executionContext)
throws ProcessExecutionException, InterruptedException {
try {
StopWatch stopWatch = new StopWatch();
stopWatch.start();
RampartProcessArgs args = this.getRampartArgs();
// Force run parallel to false if not using a scheduler
if (!executionContext.usingScheduler()) {
if (args.isRunParallel()) {
log.warn("Forcing linear execution due to lack of job scheduler");
}
args.setRunParallel(false);
}
log.info("Starting " + this.getName() + " Process");
this.results = new ArrayList<>();
// Loop through all samples to process
for (Mecq.Sample sample : args.samples) {
if (sample.failedAtStage == -1) {
File stageDir = args.getStageDir(sample);
// Ensure sample output directory exists
if (!stageDir.exists()) {
stageDir.mkdirs();
}
// Do samples specific work
TaskResult sampleResults = this.executeSample(sample, executionContext);
// Collect results
for (ExecutionResult res : sampleResults.getProcessResults()) {
results.add(res);
}
}
}
// Ensure wait log directory exists
File logDir = new File(args.outputDir, "wait_logs");
if (!logDir.exists()) {
logDir.mkdirs();
}
// If we're using a scheduler and we have been asked to run jobs
// in parallel, then we should wait for all those to complete before finishing this stage.
if (executionContext.usingScheduler() && args.runParallel) {
log.info("Running all " + this.getName() + " jobs in parallel, waiting for completion");
MultiWaitResult mrw =
this.conanExecutorService.executeScheduledWait(
results,
args.jobPrefix + "-*",
ExitStatus.Type.COMPLETED_ANY,
args.jobPrefix + "-wait",
logDir);
}
// Check all the required output files are in place (delegated to child class)
// Loop through all samples to process
for (int i = 0; i < args.samples.size(); i++) {
Mecq.Sample sample = args.samples.get(i);
if (sample.failedAtStage == -1) {
boolean valid = this.validateOutput(sample);
if (!valid) {
sample.failedAtStage = args.getStage().ordinal();
if (args.samples.size() == 1) {
throw new IOException(
"Stage " + args.getStage().name() + " failed to produce valid output.");
} else {
log.error(
"Sample "
+ sample.name
+ " failed to produce valid output for stage "
+ args.getStage().name()
+ " discontinuing pipeline for this sample.");
}
}
}
}
this.finalise();
log.info("Finished " + this.getName() + " Process");
stopWatch.stop();
this.taskResult =
new DefaultTaskResult(
"rampart-" + this.getName(), true, results, stopWatch.getTime() / 1000L);
// Output the resource usage to file
FileUtils.writeLines(
new File(logDir, args.jobPrefix + ".summary"), this.taskResult.getOutput());
return new DefaultExecutionResult(
this.taskResult.getTaskName(),
0,
new String[] {},
null,
-1,
new ResourceUsage(
this.taskResult.getMaxMemUsage(),
this.taskResult.getActualTotalRuntime(),
this.taskResult.getTotalExternalCputime()));
} catch (IOException e) {
throw new ProcessExecutionException(2, e);
}
}
@Override
public ExecutionResult execute(ExecutionContext executionContext)
throws ProcessExecutionException, InterruptedException {
try {
StopWatch stopWatch = new StopWatch();
stopWatch.start();
log.info("Starting Kmer Counting on all Reads");
// Create shortcut to args for convienience
Args args = this.getArgs();
// Force run parallel to false if not using a scheduler
if (!executionContext.usingScheduler() && args.isRunParallel()) {
log.warn("Forcing linear execution due to lack of job scheduler");
args.setRunParallel(false);
}
// Create the output directory
args.getOutputDir().mkdirs();
JobOutputMap jfCountOutputs = new JobOutputMap();
List<ExecutionResult> jobResults = new ArrayList<>();
List<ExecutionResult> allJobResults = new ArrayList<>();
// Create the output directory for the RAW datasets
File rawOutputDir = new File(args.getOutputDir(), "raw");
if (!rawOutputDir.exists()) {
rawOutputDir.mkdirs();
}
// Start jellyfish on all RAW datasets
for (Library lib : args.getAllLibraries()) {
// Execute jellyfish and add id to list of job ids
JobOutput jfOut = this.executeJellyfishCount(args, "raw", args.getOutputDir(), lib);
jobResults.add(jfOut.getResult());
allJobResults.add(jfOut.getResult());
jfCountOutputs.updateTracker("raw", jfOut.getOutputFile());
}
// Also start jellyfish on all the prep-processed libraries from MECQ
if (args.getAllMecqs() != null) {
for (Mecq.EcqArgs ecqArgs : args.getAllMecqs()) {
// Create the output directory for the RAW datasets
File ecqOutputDir = new File(args.getOutputDir(), ecqArgs.getName());
if (!ecqOutputDir.exists()) {
ecqOutputDir.mkdirs();
}
for (Library lib : ecqArgs.getOutputLibraries()) {
// Add jellyfish id to list of job ids
JobOutput jfOut =
this.executeJellyfishCount(args, ecqArgs.getName(), args.getOutputDir(), lib);
jobResults.add(jfOut.getResult());
allJobResults.add(jfOut.getResult());
jfCountOutputs.updateTracker(ecqArgs.getName(), jfOut.getOutputFile());
}
}
}
// If we're using a scheduler and we have been asked to run each job
// in parallel, then we should wait for all those to complete before continueing.
if (executionContext.usingScheduler() && args.isRunParallel()) {
log.info("Kmer counting all ECQ groups in parallel, waiting for completion");
this.conanExecutorService.executeScheduledWait(
jobResults,
args.getJobPrefix() + "-count-*",
ExitStatus.Type.COMPLETED_ANY,
args.getJobPrefix() + "-kmer-count-wait",
args.getOutputDir());
}
// Waiting point... clear job ids.
jobResults.clear();
JobOutputMap mergedOutputs = new JobOutputMap();
// Now execute merge jobs if required
for (Map.Entry<String, Set<File>> entry : jfCountOutputs.entrySet()) {
String ecqName = entry.getKey();
Set<File> fileSet = entry.getValue();
// Only merge if there's more than one library
if (fileSet.size() > 1) {
JobOutput jfOut =
this.executeJellyfishMerger(
args, ecqName, fileSet, new File(args.getOutputDir(), ecqName));
jobResults.add(jfOut.getResult());
allJobResults.add(jfOut.getResult());
mergedOutputs.updateTracker(ecqName, jfOut.getOutputFile());
}
}
// If we're using a scheduler and we have been asked to run each job
// in parallel, then we should wait for all those to complete before continueing.
if (executionContext.usingScheduler() && args.isRunParallel()) {
log.info(
"Creating merged kmer counts for all ECQ groups in parallel, waiting for completion");
this.conanExecutorService.executeScheduledWait(
jobResults,
args.getJobPrefix() + "-merge-*",
ExitStatus.Type.COMPLETED_ANY,
args.getJobPrefix() + "-kmer-merge-wait",
args.getOutputDir());
}
// Waiting point... clear job ids.
jobResults.clear();
// Combine all jellyfish out maps
jfCountOutputs.combine(mergedOutputs);
String katGcpJobPrefix = args.getJobPrefix() + "-kat-gcp";
// Run KAT GCP on everything
List<ExecutionResult> katGcpResults =
this.executeKatGcp(
jfCountOutputs,
katGcpJobPrefix,
args.getThreadsPerProcess(),
args.getMemoryPerProcess(),
args.isRunParallel());
for (ExecutionResult result : katGcpResults) {
result.setName(result.getName().substring(args.getJobPrefix().length() + 1));
jobResults.add(result);
allJobResults.add(result);
}
// If we're using a scheduler and we have been asked to run each job
// in parallel, then we should wait for all those to complete before continueing.
if (executionContext.usingScheduler() && args.isRunParallel()) {
log.info("Running \"kat gcp\" for all ECQ groups in parallel, waiting for completion");
this.conanExecutorService.executeScheduledWait(
jobResults,
katGcpJobPrefix + "*",
ExitStatus.Type.COMPLETED_ANY,
args.getJobPrefix() + "-kat-gcp-wait",
args.getOutputDir());
}
// Waiting point... clear job ids.
jobResults.clear();
log.info("Kmer counting of all reads finished.");
stopWatch.stop();
TaskResult taskResult =
new DefaultTaskResult(
"rampart-read_analysis-kmer", true, allJobResults, stopWatch.getTime() / 1000L);
// Output the resource usage to file
FileUtils.writeLines(
new File(args.getOutputDir(), args.getJobPrefix() + ".summary"), taskResult.getOutput());
return new DefaultExecutionResult(
taskResult.getTaskName(),
0,
new String[] {},
null,
-1,
new ResourceUsage(
taskResult.getMaxMemUsage(),
taskResult.getActualTotalRuntime(),
taskResult.getTotalExternalCputime()));
} catch (ConanParameterException | IOException e) {
throw new ProcessExecutionException(-1, e);
}
}
