Error in RCircos.Validate.Genomic.Data(genomic.data, plot.type)

[blaiseli]

Dear Bo Han,

My run of piPipes dna ended as follows:

[2015-09-18 21:09:09 CEST] Discovering Variation by BreakDancer using BWA output
[2015-09-18 23:43:31 CEST] Draw Cisco plot to summarize the finding
Loading required package: RCircos

RCircos.Core.Components initialized.
Type ?RCircos.Reset.Plot.Parameters to see how to modify the core components.

Warning message:
In order(as.numeric(sub("chr", "", chr.names))) :
  NAs introduced by coercion
Some chromosomes are in genomic data only and have been removed.


Maximum lables for  chr4 is 2 . Extra ones are ignored.
Maximum lables for  chr2LHet is 0 . Extra ones are ignored.
Maximum lables for  chr2RHet is 5 . Extra ones are ignored.
Maximum lables for  chr3LHet is 4 . Extra ones are ignored.
Maximum lables for  chr3RHet is 4 . Extra ones are ignored.
Maximum lables for  chrXHet is 0 . Extra ones are ignored.

Some chromosomes are in genomic data only and have been removed.


Maximum lables for  chr4 is 2 . Extra ones are ignored.
Maximum lables for  chr2LHet is 0 . Extra ones are ignored.
Maximum lables for  chr2RHet is 5 . Extra ones are ignored.
Maximum lables for  chr3LHet is 4 . Extra ones are ignored.
Maximum lables for  chr3RHet is 4 . Extra ones are ignored.
Maximum lables for  chrXHet is 0 . Extra ones are ignored.

    Chr Start   End TransposonName TransposonDirection     Class VariantSupport
1 chr2L  7106  7606          TAHRE               sense        2p             43
2 chr2L 19524 20024          R1_DM               sense singleton              1
3 chr2L 23386 23886             FW           antisense singleton              1
4 chr2L 25651 25683           I_DM               sense       1p1            236
5 chr2L 26220 26720        BLOOD_I               sense singleton              1
6 chr2L 26500 27000     INVADER4_I           antisense singleton              1
  Frequency Junction1 Junction1Support Junction2 Junction2Support X5._Support
1    0.8269      7524               26      7524                0           0
2    0.0039     19774                0     19774                0           1
3    0.0042     23636                0     23636                0           1
4    0.8459     25661               13     25661                0         139
5    0.0030     26470                0     26470                0           1
6    0.0030     26750                0     26750                0           1
  X3._Support
1          17
2           0
3           0
4          84
5           0
6           0
Some chromosomes are in genomic data only and have been removed.

chr3RHet 2517343 2517843 
Error in RCircos.Validate.Genomic.Data(genomic.data, plot.type) : 
  Error! Location is outside of chromosome length.
Calls: RCircos.Tile.Plot ... RCircos.Get.Plot.Data -> RCircos.Validate.Genomic.Data
Execution halted
[2015-09-18 23:43:36 CEST] Finished running piPipes Genome-Seq pipeline version 1.0.1
[2015-09-18 23:43:36 CEST] ---------------------------------------------------------------------------------

The problem seems to correspond to the following line of the *.bwa-aln.insertion.refined.bp.summary file:

chr3RHet    2517343 2517843 Transib4    antisense   2p  7   1.0000  2517593 0   2517593 0   7   0

I'm using option -g dm3 for the genome.