Error in Qualimap RNA-seq QC

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.


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 .


Execution resulted in the following messages:

Fatal error: Exit code 255 ()

Tool generated the following standard error:

Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m
Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m
Failed to run rnaseq
java.lang.IllegalArgumentException: Comparison method violates its general contract!
at java.base/java.util.TimSort.mergeLo(
at java.base/java.util.TimSort.mergeAt(
at java.base/java.util.TimSort.mergeForceCollapse(
at java.base/java.util.TimSort.sort(
at java.base/java.util.Arrays.sort(
at org.bioinfo.ngs.qc.qualimap.common.TranscriptDataHandler.createHelperMaps(
at org.bioinfo.ngs.qc.qualimap.common.TranscriptDataHandler.constructTranscriptsMap(
at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.loadRegionsFromGTF(
at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.initRegions(
at org.bioinfo.ngs.qc.qualimap.main.RnaSeqQcTool.execute(
at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(


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

Any ideas?

Hi. Were you able to figure out how to get rid of the error? I’m getting a similar warning when I try to run Qualimap on the terminal.

In the end I ended up using other tools, couldn’t solve this in the online instance of galaxy :frowning:

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