protected JobOutput executeJellyfishMerger( Args args, String ecqName, Set<File> fileSet, File outputDir) throws InterruptedException, ProcessExecutionException, ConanParameterException, IOException { String suffix = "jellyfish_" + ecqName + "_all.jf31_0"; String jobName = args.getJobPrefix() + "-merge-" + suffix; List<File> files = new ArrayList<>(); files.addAll(fileSet); File outputFile = new File(outputDir, suffix); JellyfishMergeV11 jellyfishMerge = this.makeJellyfishMerge(files, outputFile, args.getOrganism()); ExecutionResult id = this.conanExecutorService.executeProcess( jellyfishMerge, args.getOutputDir(), jobName, args.getThreadsPerProcess(), args.getMemoryPerProcess(), args.isRunParallel()); id.setName("merge-" + suffix); return new JobOutput(id, outputFile); }