Failed to run (after 15 min) rnaseq

[Emmanuel Prestat]

Dear qualimap forum,
first, thanks to the qulimap team for this wonderful work.

I have trouble with the rnaseq mode: the job starts well but after a significant time, it says the bam is empty (it is not).
Could you help me to understand?

Java memory size is set to 40G
Launching application...

QualiMap v.2.2
Built on 2016-01-29 12:10

Selected tool: rnaseq
Fri Aug 05 15:10:54 CEST 2016        WARNING    Output folder already exists, the results will be saved there

Initializing regions from /data/BioInfo_Data/Mus_Musculus/mm10/mm10.gtf...

Initialized 100000 regions...
Initialized 200000 regions...
Initialized 300000 regions...
Initialized 400000 regions...
Initialized 500000 regions...
Initialized 600000 regions...
Initialized 700000 regions...
Initialized 800000 regions...
Initialized 900000 regions...
Initialized 1000000 regions...
Initialized 1100000 regions...
Initialized 1200000 regions...
Initialized 1300000 regions...
Initialized 1400000 regions...
Initialized 1500000 regions...
Initialized 1600000 regions...

Initialized 1608984 regions it total

Starting constructing transcripts for RNA-seq stats...
Warning! Transcript DQ713846 has incorrect exon coordinates. Transcript skipped...
Warning! Transcript AJ459715 has incorrect exon coordinates. Transcript skipped...
Warning! Transcript AJ459704 has incorrect exon coordinates. Transcript skipped...
Warning! Transcript AJ459707 has incorrect exon coordinates. Transcript skipped...
Warning! Transcript AJ459701 has incorrect exon coordinates. Transcript skipped...
Warning! Transcript AJ459703 has incorrect exon coordinates. Transcript skipped...
Warning! Transcript AJ459702 has incorrect exon coordinates. Transcript skipped...
[....]
Failed to run rnaseq
java.lang.RuntimeException: BAM file is empty.
    at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.run(ComputeCountsTask.java:493)
    at org.bioinfo.ngs.qc.qualimap.process.RNASeqQCAnalysis.run(RNASeqQCAnalysis.java:68)
    at org.bioinfo.ngs.qc.qualimap.main.RnaSeqQcTool.execute(RnaSeqQcTool.java:188)
    at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:187)
    at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:111)

Thanks,
Emmanuel

[Konstantin Okonechnikov]

Hi Emmanuel,

it could be that the chromosome names in the annotation do not pass the names in the BAM file.

Where the annotation file was downloaded from? There are some strange warning messages there, maybe this has influence and the annotations are ignored.

Also, could you perhaps share a small random subsample from the BAM file or the header so I can check it?

--

  Konstantin

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[Emmanuel Prestat]

Hi Konstantin,

thanks for your answer.

The issue was indeed the chromosome naming.

It works perfectly now,

Best,

Emmanuel

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