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View Code? Open in Web Editor NEWRNA-SeQC v1 — Please upgrade to v2: https://github.com/broadinstitute/rnaseqc
RNA-SeQC v1 — Please upgrade to v2: https://github.com/broadinstitute/rnaseqc
I am trying to run RNA-SeQC on one RNA-seq sample. While I can get the program to execute, the program finds no expressed genes, which I find hard to believe. Is there expanded documentation for this tool anywhere? The Broad page suggests that documentation does exist, but if you go to the link, the page does not exist. In order to troubleshoot this problem, I think I need to understand a bit more how it works and what it is expecting. Please advise and thank you.
Hello,
My lab has been using the original RNAseqc for a while and likes the tool. I had been looking for the source code for a long time and just came across this. It looks like it would be pretty easy to migrate the code to a more modern build, java version and picard/gatk versions. I can fork the repo and do this. I'm just writing to see if anyone is actively watching this repo and if there was interest in some discussion around this?
Hi,
I am using RNA-SeQC like this:
$ java -Xmx6g -jar RNA-SeQC_v1.1.8.jar \
-s PPTC-AF03-XTP1-A-1-0-R_sample_file.txt \
-t Homo_sapiens.GRCh37.71.hap.ERCC.gtf \
-r Homo_sapiens.GRCh37.71.hap.ERCC.sm.fa \
-o PPTC-AF03-XTP1-A-1-0-R
Java version
java -version
openjdk version "1.8.0_121"
OpenJDK Runtime Environment (Zulu 8.20.0.5-linux64) (build 1.8.0_121-b15)
OpenJDK 64-Bit Server VM (Zulu 8.20.0.5-linux64) (build 25.121-b15, mixed mode)
Here is the log with the error:
RNA-SeQC v1.1.8.1 07/11/14
Creating rRNA Interval List based on given GTF annotations
Retriving contig names from reference
contig names in reference: 185
Loading GTF for Read Counting
Converting to refGene
Transcript objects to RefGen format: 6 s
Running IntronicExpressionReadBlock Walker ....
Exception in thread "main" java.lang.ExceptionInInitializerError
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.<init>(GenomeAnalysisEngine.java:146)
at org.broadinstitute.sting.gatk.CommandLineExecutable.<init>(CommandLineExecutable.java:53)
at org.broadinstitute.sting.gatk.CommandLineGATK.<init>(CommandLineGATK.java:55)
at org.broadinstitute.cga.rnaseq.gatk.GATKTools.runIntronReadCount(GATKTools.java:216)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runRegionCounting(ReadCountMetrics.java:244)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runReadCountMetrics(ReadCountMetrics.java:59)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(RNASeqMetrics.java:225)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:171)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:139)
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: could not create class file from ArrayBufferView.class
at org.reflections.Reflections.scan(Reflections.java:166)
at org.reflections.Reflections.<init>(Reflections.java:91)
at org.broadinstitute.sting.utils.classloader.PluginManager.<clinit>(PluginManager.java:79)
... 9 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: could not create class file from ArrayBufferView.class
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at org.reflections.Reflections.scan(Reflections.java:162)
... 11 more
Caused by: java.lang.RuntimeException: could not create class file from ArrayBufferView.class
at org.reflections.scanners.AbstractScanner.scan(AbstractScanner.java:41)
at org.reflections.Reflections$2.run(Reflections.java:149)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: invalid constant type: 15
at javassist.bytecode.ConstPool.readOne(ConstPool.java:1023)
at javassist.bytecode.ConstPool.read(ConstPool.java:966)
at javassist.bytecode.ConstPool.<init>(ConstPool.java:127)
at javassist.bytecode.ClassFile.read(ClassFile.java:693)
at javassist.bytecode.ClassFile.<init>(ClassFile.java:85)
at org.reflections.adapters.JavassistAdapter.createClassObject(JavassistAdapter.java:86)
at org.reflections.adapters.JavassistAdapter.createClassObject(JavassistAdapter.java:22)
at org.reflections.scanners.AbstractScanner.scan(AbstractScanner.java:38)
... 6 more
Any help would be much appreciated.
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