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AnalyzeCovariates would crash with 'too many open files' exception when spawning Rscript jobs for every read group at once. It now waits for some to finish before spawning the rest. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2508 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-06 14:19:02 +00:00
parent 588006ee92
commit 71ecbe75d7
1 changed files with 26 additions and 5 deletions
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31
java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
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@ -237,24 +237,45 @@ class AnalyzeCovariatesCLP extends CommandLineProgram {
String readGroup = readGroupKey.toString();
System.out.println("Analyzing read group: " + readGroup);
Process p = null;
// for each covariate
for( int iii = 1; iii < requestedCovariates.size(); iii++ ) {
Covariate cov = requestedCovariates.get(iii);
try {
if( iii == 1 ) {
// Analyze reported quality
Process p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_QualityScoreCovariate.R" + " " +
p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_QualityScoreCovariate.R" + " " +
OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
IGNORE_QSCORES_LESS_THAN); // The third argument is the Q scores that should be turned pink in the plot because they were ignored
} else { // Analyze all other covariates
Process p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_OtherCovariate.R" + " " +
p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_OtherCovariate.R" + " " +
OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice
}
} catch (IOException e) {
e.printStackTrace();
System.exit(-1);
} catch (IOException ex) {
try {
Thread.sleep(1600); // wait for 1.6 seconds and then try to spawn the process again
if( iii == 1 ) {
// Analyze reported quality
p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_QualityScoreCovariate.R" + " " +
OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
IGNORE_QSCORES_LESS_THAN); // The third argument is the Q scores that should be turned pink in the plot because they were ignored
} else { // Analyze all other covariates
p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_OtherCovariate.R" + " " +
OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice
}
} catch (InterruptedException e) {
e.printStackTrace();
System.exit(-1);
} catch (IOException e) {
e.printStackTrace();
System.exit(-1);
}
}
}
} else {
break;