Chromosome, start and end vector must have the same lengths

[zgtman]

Dear creators of ExomeDepth,

I am facing very curious Error form my Agilent WES BAM files.

Can anybody tell me why I have ths kind of error?

Error in CallCNVs(x = all_exons, transition.probability = 10^-4, chromosome = countdf$chromosome,  : 
  Chromosome, start and end vector must have the same lengths.
Calls: CallCNVs -> CallCNVs
In addition: Warning messages:
1: In aod::betabin(data = data.for.fit, formula = as.formula(formula),  :
  The data set contains at least one line with weight = 0.

2: In model.matrix.default(mt, mfb, contrasts) :
  non-list contrasts argument ignored
3: In aod::betabin(data = data.for.fit, formula = as.formula(formula),  :
  The data set contains at least one line with weight = 0.

4: In model.matrix.default(mt, mfb, contrasts) :
  non-list contrasts argument ignored
5: In aod::betabin(data = data.for.fit, formula = as.formula(formula),  :
  The data set contains at least one line with weight = 0.

6: In model.matrix.default(mt, mfb, contrasts) :
  non-list contrasts argument ignored
7: In model.matrix.default(mt, mfb, contrasts) :
  non-list contrasts argument ignored
8: In model.matrix.default(mt, mfb, contrasts) :
  non-list contrasts argument ignored
9: In aod::betabin(data = data.for.fit, formula = as.formula(formula),  :
  The data set contains at least one line with weight = 0.

10: In model.matrix.default(mt, mfb, contrasts) :
  non-list contrasts argument ignored
Execution halted

Thank you so much for any help,

Paul.

[master-noddy]

I also got this same error. Convert the exon file into a tab-separated file and then try running the script

[lmanchon]

this is what i have done and nothing change for me:

Error in CallCNVs(x = all.exons, transition.probability = trans_prob, : Chromosome, start and end vector must have the same lengths. De plus : Warning messages: 1: In aod::betabin(data = data.for.fit, formula = as.formula(formula), : The data set contains at least one line with weight = 0. bla bla bla

short extract of my bed: chr Start end Gene chr1 11868 12227 DDX11L1 chr1 12612 12721 DDX11L1 chr1 13220 14409 DDX11L1 chr1 14403 14501 WASH7P chr1 15004 15038 WASH7P chr1 15795 15947 WASH7P chr1 16606 16765 WASH7P chr1 16857 17055 WASH7P chr1 17232 17368 WASH7P chr1 17368 17436 MIR6859-1 chr1 17605 17742 WASH7P chr1 17914 18061 WASH7P chr1 18267 18366 WASH7P chr1 24737 24891 WASH7P chr1 29533 29570 WASH7P chr1 29553 30039 MIR1302-2HG chr1 30365 30503 MIR1302-2 chr1 30563 30667 MIR1302-2HG chr1 30975 31097 MIR1302-2HG chr1 34553 35174 FAM138A chr1 35276 35481 FAM138A chr1 35720 36081 FAM138A

[uhany2]

I am getting the same error, can anyone please help?

[mnb29]

I have the same error. Was this ever solved?

[Jolleboll]

Hello. The error message is incomplete. It should say:

Chromosome, name, start and end vectors must have the same lengths.

My problem was that my "names" vector was called "exon", so copy-pasting from the vignette meant my names-vector had length zero, which indeed is not the same as the other three vectors. But, the error message is incomplete, as I said.

[vplagnol]

Thanks- it looks like I need to update the error message! Let me try to do that now.

[vplagnol]

And version 1.1.17 should have an updated error message. You can try from github. It may not quite warrant a CRAN update, but I'll try to bundle that with whatever additional fixes before I update on the repo.

Thanks again!