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GATK UnifiedGenotyper freeze when run by Java application

Hello,

I have a simple run.sh bash script which runs gatk UnifiedGenotyper on 40 bam files. If I run the script manually, analysis finish without problem. If I start the analysis through Java script test.java, it freezes in the middle of the processing (approx. 20th sample), also depending on -nt and -nct values. If I kill the Java script after freezing, the analysis continue on the next sample without problems.

Do you have any suggestions where is the problem & how to fix it?

It's important for me to run the script through Java.

My version of gatk is 3.6; Java 1.8
samples have average coverage 35000

run.sh

!/bin/bash

for file in path/to/*.sorted.bam
do
FNAME=$(basename "$file");
java -jar GenomeAnalysisTK.jar -nt 4 -stand_emit_conf 10 -stand_call_conf 25 -nct 25 -maxAltAlleles 15 --output_mode EMIT_VARIANTS_ONLY --max_deletion_fraction 0.001 --min_indel_fraction_per_sample 0.001 -gt_mode DISCOVERY -T UnifiedGenotyper -R path/to/bundle_GATK/b37/b37/human_g1k_v37.fasta --disable_auto_index_creation_and_locking_when_reading_rods --genotype_likelihoods_model BOTH -ploidy 2 -L 17:1-9999999 -dcov 9999999 --logging_level INFO -I $file -o path/to/output/${FNAME}.genotyper.vcf --log_to_file path/to/output/${FNAME}.log
done

test.java
package test;

import java.io.File;

public class Test
{

public static void main(String[] args)
{
    File currentDir = new File(".");

    try
    {
        Process process = Runtime.getRuntime().exec(currentDir.getAbsolutePath() + File.separator + "run.sh");

        process.waitFor();
    }
    catch (Exception e)
    {
        System.out.println(e.getMessage());
    }
}

}

Thanks a lot

nikosh

Issue · Github
by Sheila

Issue Number
1445
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Answers

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