Qualimap counts error!

[Hoyoung Ghang]

Hi,

Good and easy tool to get mapping statistics.

Tools, 'bamqc' and 'comp-count', work good. But when I tried the tool 'counts', there was some error as follows,

[lsw@localhost analysis]$ /home/lsw/local/qualimap/qualimap counts -d1 ./result_statistics_tmp/N3_FCC2084ACXX_L1_HUMaaeTAFRABPEI-62 -d2 ./result_statistics_tmp/C3_FCC2084ACXX_L2_HUMaaeTAGRABPEI-71 -i /Bio2/pipelines/transcriptome/lib/human.genes.biotypes -n1 N3 -n2 C3 -outdir result_statistics_RNAseq/N3_VS_C3 -outformat PDF -s human --java-mem-size=6G
Java memory size is set to 6G
Launching application...

QualiMap v.0.8
Built on 2014-03-05 17:17

Selected tool: counts
Tue Apr 22 09:16:57 KST 2014        WARNING    output folder already exists
Command: Rscript /home/lsw/local/qualimap/scripts/qualimapRscript.r --homesrc /home/lsw/local/qualimap/scripts --data1 ./result_statistics_tmp/N3_FCC2084ACXX_L1_HUMaaeTAFRABPEI-62 --name1 "N3" --data2 ./result_statistics_tmp/C3_FCC2084ACXX_L2_HUMaaeTAGRABPEI-71 --name2 "C3" --info /Bio2/pipelines/transcriptome/lib/human.genes.biotypes --threshold 5 -o /tmp/qualimap1398125817516/
Failed to analyze counts
java.lang.RuntimeException: The process returned non-zero status!
    at org.bioinfo.ngs.qc.qualimap.process.CountsAnalysis.run(CountsAnalysis.java:157)
    at org.bioinfo.ngs.qc.qualimap.main.CountsQcTool.execute(CountsQcTool.java:176)
    at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:177)
    at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:98)

Thus I tried with some optional changes and get results when I tried with only one sample just using '-d1' not with 'd2'.

Anyone has some idea?