Qualimap countsQC error

[Aaron Jex]

Hello,

I'm having a problem with running qualimap counts. I have R version 2.14.0 installed as well as the required dependcies (installed using the dependencies Rscript that comes with the qualimap code).

Using the test data sets (mouse_counts_ensembl.txt and GlcN_countsqc_input.txt) and copy and pasting the command to run countsQC from the Qualimap manual:

qualimap counts -d GlcN_countsqc_input.txt -c -s mouse -outdir glcn_mice_counts

I get the following error

Java memory size is set to 1200M

Launching application...

QualiMap v.2.2-dev

Built on 2015-11-26 10:30

Selected tool: counts

Rscript /media/Space2/home/aaron/Software/qualimap-build-26-11-15/scripts/countsQC.r --homedir /media/Space2/home/aaron/Software/qualimap-build-26-11-15/scripts --input /tmp/qualimap1449108619657//input.txt -k 5 --info /media/Space2/home/aaron/Software/qualimap-build-26-11-15/species/mouse.ens68.txt --compare -o /tmp/qualimap1449108619657/

Reading input data using input description from /tmp/qualimap1449108619657//input.txt

Loaded counts for  21405  features

Num samples: 6

Conditions:

  Conditions

1      nGlcn

2      nGlcn

3      nGlcn

4      pGlcn

5      pGlcn

6      pGlcn

Compare conditions  TRUE

Loading annotations from  /media/Space2/home/aaron/Software/qualimap-build-26-11-15/species/mouse.ens68.txt

Loaded annoations for  37315 genes

21178 out of 21405 annotations from counts file found in annotations file

'data.frame':   21405 obs. of  6 variables:

 $ nGlcn01: int  641 73 2359 39 1 292 421 16 812 445 ...

 $ nGlcn02: int  542 17 1563 165 0 184 300 5 566 273 ...

 $ nGlcn03: int  776 47 2497 124 3 220 380 7 727 375 ...

 $ pGlcn01: int  787 15 1522 127 0 199 353 7 629 406 ...

 $ pGlcn02: int  491 32 2126 83 6 228 316 6 569 305 ...

 $ pGlcn03: int  791 29 2149 144 1 237 393 6 784 410 ...

 - attr(*, "factors")= Factor w/ 2 levels "nGlcn","pGlcn": 1 1 1 2 2 2

[1] 21405     6

Init NOISeq data...

Error in readData(data = counts, length = gene.length, gc = gene.gc, biotype = gene.biotypes,  :

  unused argument(s) (gc = gene.gc)

Execution halted

Failed to run counts

java.lang.RuntimeException: The RScript process finished with error.

 Check log for details.

        at org.bioinfo.ngs.qc.qualimap.process.CountsQcAnalysis.run(CountsQcAnalysis.java:119)

        at org.bioinfo.ngs.qc.qualimap.main.CountsQcTool.execute(CountsQcTool.java:182)

        at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:187)

        at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:111)

Thu Dec 03 13:10:24 AEDT 2015           WARNING Cleanup output dir

I have tried Qualimap v2.13.2, Qualimap v2.13.3 and the 23-09-2015 build and 26-11-2015 available through https://bitbucket.org/kokonech/qualimap/downloads

I've also tried replacing qualimapRscript.r with the version found here.

https://groups.google.com/forum/#!msg/qualimap/G5GLfqbFflE/bu-4UvdBa6YJ

I get the same error each time.

The error message mentions checking several logs for more details, but I don't know if those are written to a temp directory or if this relates to something else. No files appear to be written to my working directory

I note that the error relating to "readData(data = counts, length = gene.length, gc = gene.gc, biotype = gene.biotypes, " relates to the countsQC.r script, but I have no rscripting ability, so there isn't much tinkering I can do (even assuming that this is actually the problem - which I'm betting it is not).

Would anyone be able to help please?  The only other thing I can think of is that there is some R compatibility issue, but the QualiMap map says R 2.14 and above, so in theory I should be okay.

Best wishes

Aaron

[Aaron Jex]

Ah hah. I might as well leave this up here in case anyone else gets caught out by this. Has to be the latest version of R. Running R version 3.1.1. Both the test data and my own data run perfectly now.

Aaron

[Konstantin Okonechnikov]

Thanks a lot for the info! The requirement for R version will be also updated in the documentation in next release. 

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