countQC saturation error

[Alena Dobiášová]

Hello,

I have a new problem with count QC tool.

I loaded the same data as last time but something is wrong and this time I really dont know how to find out what, because clearly data loading works fine. I have installed all 6 required R libraries from http://qualimap.bioinfo.cipf.es/doc_html/intro.html#install-r. I checked the code in countsQC.r and everything up to explo.plot(saturation, toplot = 1, samples = NULL) is working. This line causes the error.

Thank you in advance, Alena

Java memory size is set to 5G
Launching application...

QualiMap v.2.1.1
Built on 2015-06-15 14:19

Selected tool: counts
WARNING: The sample name "1560" will be replaced with name "sample_1560" due to NOISeq issues
WARNING: The sample name "1587" will be replaced with name "sample_1587" due to NOISeq issues
WARNING: The sample name "1646" will be replaced with name "sample_1646" due to NOISeq issues
WARNING: The sample name "1789" will be replaced with name "sample_1789" due to NOISeq issues
WARNING: The sample name "1638" will be replaced with name "sample_1638" due to NOISeq issues
WARNING: The sample name "1794" will be replaced with name "sample_1794" due to NOISeq issues
WARNING: The sample name "2103" will be replaced with name "sample_2103" due to NOISeq issues
WARNING: The sample name "2251" will be replaced with name "sample_2251" due to NOISeq issues
WARNING: The sample name "2212" will be replaced with name "sample_2212" due to NOISeq issues
WARNING: The sample name "1883" will be replaced with name "sample_1883" due to NOISeq issues
Rscript /seqtools/qualimap_v2.1.1/scripts/countsQC.r --homedir /seqtools/qualimap_v2.1.1/scripts --input /tmp/qualimap1441702211411//input.txt -k 5 --info /Data/SeqReference/Homo_sapiens.GRCh37.75.qlmpcntinfo.txt -o /tmp/qualimap1441702211411/
Reading input data using input description from /tmp/qualimap1441702211411//input.txt
Loaded counts for  63682  features
Num samples: 20
Conditions:
   Conditions
1   condition
2   condition
3   condition
4   condition
5   condition
6   condition
7   condition
8   condition
9   condition
10  condition
11  condition
12  condition
13  condition
14  condition
15  condition
16  condition
17  condition
18  condition
19  condition
20  condition

Compare conditions  FALSE
Loading annotations from  /Data/SeqReference/Homo_sapiens.GRCh37.75.qlmpcntinfo.txt
Loaded annoations for  63677 genes
63677 out of 63682 annotations from counts file found in annotations file
'data.frame':    63682 obs. of  20 variables:
 $ D1         : int  13 0 790 242 62 1 0 0 244 3192 ...
 $ HA3        : int  14 0 741 279 332 8 2 98 415 9915 ...
 $ HA4        : int  0 0 98 264 56 548 41 0 201 128 ...
 $ HR1        : int  47 0 676 176 147 44 16 12 518 6127 ...
 $ N3         : int  26 0 231 142 119 2 41 11 113 1734 ...
 $ N5         : int  13 0 433 93 76 12210 13 434 369 1339 ...
 $ N6         : int  108 0 165 13 40 1391 34 523 64 38 ...
 $ N8         : int  40 0 75 1 109 15 7 1 4 125 ...
 $ sample_1560: int  15 0 483 181 246 400 5 30 259 2863 ...
 $ sample_1587: int  3 0 1038 447 520 375 5 81 286 3071 ...
 $ sample_1646: int  32 0 490 264 230 198 6 17 307 3353 ...
 $ sample_1789: int  40 0 867 173 177 53 3 22 600 1296 ...
 $ H          : int  24 0 470 173 294 610 114 274 1958 915 ...
 $ M          : int  6 0 1993 1385 1440 2167 11 125 2624 14150 ...
 $ sample_1638: int  0 0 596 338 404 131 11 19 512 4746 ...
 $ sample_1794: int  0 0 533 325 343 84 67 14 720 2460 ...
 $ sample_2103: int  2 0 1012 322 660 165 29 231 866 2207 ...
 $ sample_2251: int  66 0 2725 1158 1030 4679 109 331 2437 12526 ...
 $ sample_2212: int  9 0 2124 958 987 1640 43 110 1652 10114 ...
 $ sample_1883: int  3 0 2303 166 250 1353 2 49 1252 1925 ...
 - attr(*, "factors")= Factor w/ 1 level "condition": 1 1 1 1 1 1 1 1 1 1 ...
[1] 63682    20
Init NOISeq data...

Draw global plots...
Compute counts density...
Compute scatterplots..
Compute saturation..
Error in saturation.plot(object@dat, samples = samples, toplot = toplot,  :
  object 'sat' not found
Calls: explo.plot -> explo.plot -> .local -> saturation.plot
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:186)
    at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:111)

[Konstantin Okonechnikov]

Hi Alena,

thanks a lot for the report!

The problem occurs due to update of NOISeq package. The saturation plot function now has a bit different control - samples list must be provided in detail.

I fixed the issue. Could you please check if everything works fine now?

The link to the latest snapshot:

https://bitbucket.org/kokonech/qualimap/downloads/qualimap-build-08-09-15.tar.gz

--

  Konstantin

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