RNA-SeQC error shortly after start

Question

[wbliu]

Dear forum:

I've been trying to running RNA-SeQC and I believe I have done all the necessary steps to prepare the input files. The BAM files were ordered and indexed. The reference fasta file is also indexed. The GTF file was downloaded from Emsembl and the rows without the "transcript_id" fields were temporarily removed. The chromosomes are 1,2,.... I got the following error:

Exception in thread "main" java.lang.ExceptionInInitializerError
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.<init>(GenomeAnalysisEngine.java:160)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.<init>(CommandLineExecutable.java:53)
        at org.broadinstitute.sting.gatk.CommandLineGATK.<init>(CommandLineGATK.java:54)
        at org.broadinstitute.cga.rnaseq.gatk.GATKTools.runIntronReadCount(GATKTools.java:203)
        at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runRegionCounting(ReadCountMetrics.java:220)
        at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runReadCountMetrics(ReadCountMetrics.java:59)
        at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(RNASeqMetrics.java:211)
        at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:162)
        at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:133)
Caused by: java.lang.NullPointerException
        at org.reflections.Reflections.scan(Reflections.java:220)
        at org.reflections.Reflections.scan(Reflections.java:166)
        at org.reflections.Reflections.<init>(Reflections.java:94)
        at org.broadinstitute.sting.utils.classloader.PluginManager.<clinit>(PluginManager.java:77)
        ... 9 more

My script is like this:

(In the PBS directive part, I requested nodes=1:ppn=4,walltime=4:00:00,mem=24g.)

module load samtools/1.4
module load jdk/1.7.0_75
module load gatk/3.5-0-jkd8
module load RNA_SeQC/1.1.9
module load bwa/0.7.15

java -jar /risapps/noarch/RNA_SeQC/1.1.9/RNA-SeQC.jar   -o results  -r Homo_sapiens_assembly19.fasta     single.end=no   -s "myID|myBam.bam|test"  -t Homo_sapiens.GRCh37.87.gtf

(It ran about 40 s before it terminated. Two files, refGene.txt and rRNA_intervals.list, were generated during this time. Using Java 1.8.0 makes the error come even earlier. A colleague suggested using 1.7.0)

Any help/hint will be greatly appreciated!

[Ram]

I'd recommend contacting your HPC team and having them check out the job diagnostics. Sometimes java errors out at a level that is not available to any log file. An example would be if a tmp dir were full or java was unable to get the JVM going owing to insufficient memory.

[wbliu]

Thanks RamRS! I will ask them to check it.