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 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?

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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