# Error in Qualimap RNA-seq QC

**URL:** https://help.galaxyproject.org/t/error-in-qualimap-rna-seq-qc/4549
**Category:** usegalaxy.org support
**Tags:** troubleshooting, quality-control
**Created:** [October 2, 2020, 12:45am UTC](https://help.galaxyproject.org/t/error-in-qualimap-rna-seq-qc/4549 "2020-10-02T00:45:43Z")
**Posts on this page:** 1
**Showing post:** 1

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### Author: ![GACG1](https://avatars.discourse-cdn.com/v4/letter/g/7c8e57/32.png) [@GACG1](https://help.galaxyproject.org/u/GACG1)
#### Post date: [October 2, 2020, 12:45am UTC](https://help.galaxyproject.org/t/error-in-qualimap-rna-seq-qc/4549/1 "2020-10-02T00:45:43Z")

</div>

Hello everyone!

I’m trying to do QC on my RNAseq samples, and after mapping with STAR (no gene counts, 2-pass, hg38 with GFF file for spli junctions) and passing the BAM file to Qualimap RNA-seq QC, I get a error.  
The problem is that the program doesn’t even spit the error, as seen in the image.

 ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/4/48a16d45e624e8c5742b8fc9645b9b551562c07b.png)  
"

Java memory size is set to 1200M  
Launching application…

detected environment java options -Djava.awt.headless=true -Xmx7680m  
QualiMap v.2.2.2-dev  
Built on 2019-11-11 14:05

Selected tool: rnaseq  
Initializing regions from features.gtf…

Initialized 1

"

Upon further inspection, this is the error:  
"

## Dataset Error Report

An error occurred while running the tool **toolshed.g2.bx.psu.edu/repos/iuc/qualimap\_rnaseq/qualimap\_rnaseq/2.2.2d+galaxy1**.

### Details

Execution resulted in the following messages:

Fatal error: Exit code 255 ()

Tool generated the following standard error:

Picked up \_JAVA\_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/031/100/31100658/\_job\_tmp -Xmx7g -Xms256m  
Picked up \_JAVA\_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/031/100/31100658/\_job\_tmp -Xmx7g -Xms256m  
Failed to run rnaseq  
java.lang.IllegalArgumentException: Comparison method violates its general contract!  
at java.base/java.util.TimSort.mergeLo(TimSort.java:781)  
at java.base/java.util.TimSort.mergeAt(TimSort.java:518)  
at java.base/java.util.TimSort.mergeForceCollapse(TimSort.java:461)  
at java.base/java.util.TimSort.sort(TimSort.java:254)  
at java.base/java.util.Arrays.sort(Arrays.java:1441)  
at org.bioinfo.ngs.qc.qualimap.common.TranscriptDataHandler.createHelperMaps(TranscriptDataHandler.java:652)  
at org.bioinfo.ngs.qc.qualimap.common.TranscriptDataHandler.constructTranscriptsMap(TranscriptDataHandler.java:175)  
at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.loadRegionsFromGTF(ComputeCountsTask.java:702)  
at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.initRegions(ComputeCountsTask.java:608)  
at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.run(ComputeCountsTask.java:479)  
at org.bioinfo.ngs.qc.qualimap.process.RNASeqQCAnalysis.run(RNASeqQCAnalysis.java:68)  
at org.bioinfo.ngs.qc.qualimap.main.RnaSeqQcTool.execute(RnaSeqQcTool.java:221)  
at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)  
at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)

"

I’ve used the BAM file that STAR generates and the same GFF reference I used to align with STAR.

Any ideas?

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