search

NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
9 stars 9 forks source link

Upgrade to Qualimap 2.0 #44

Closed parlundin closed 9 years ago

parlundin commented 9 years ago

Qualimap bamQC terminates with ArrayIndexOutOfBoundsException when to many reads. This issue should be fixed in latest version of Qualimap 2.0

java.lang.ArrayIndexOutOfBoundsException: -452499825 at java.util.ArrayList.elementData(ArrayList.java:371) at java.util.ArrayList.get(ArrayList.java:384) at org.bioinfo.ngs.qc.qualimap.beans.BamStats.computeInsertSizeHistogram(BamStats.java:975) at org.bioinfo.ngs.qc.qualimap.beans.BamStats.computeHistograms(BamStats.java:793) at org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run(BamStatsAnalysis.java:488) at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:211) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:177) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:102)

johandahlberg commented 9 years ago

@parlundin Once you've tried running with Qualimap 2.0, could you confirm here that that actually worked? Would be good to know before updating.

parlundin commented 9 years ago

I ran it on the merged bam file for the sample that failed with previous version, it worked fine. @ewels suggested that we add:

Would be good if we can run it with this parameter: http://qualimap.bioinfo.cipf.es/doc_html/analysis.html#input-gc-content

-gd,--genome-gc-distr <arg>          Species to compare with genome GC
                                  distribution. Possible values: HUMAN or
                                  MOUSE.

I will run the recal bam file with that parameter now.

johandahlberg commented 9 years ago

Ok. Great. Will also add your suggested new parameter once I get around to this.

johandahlberg commented 9 years ago

I think that this should be fixed now. Will wait for confirmation from @parlundin, and then I'll close this.