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RamsinghLab / atacseeker_app

Illumina BaseSpace ATACseq pipeline.
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plotRegion not working. #7

Closed asifzubair closed 8 years ago

asifzubair commented 8 years ago

I got the following error related to plotRegion when I tried running the App on BaseSpace:

label: bed_track_view (with options) 

List of 1
 $ echo: logi FALSE

.Quitting from lines 404-406 (atacseeker.Rmd) 
Error in coverage(x)/metadata(x)$totals : 
  non-numeric argument to binary operator
Calls: <Anonymous> ... GRangesList -> lapply -> lapply -> FUN -> as -> .class1
In addition: Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence
  chrUn_gl000223. Note that only ranges located on a non-circular
  sequence whose length is not NA can be considered out-of-bound
  (use seqlengths() and isCircular() to get the lengths and
  circularity flags of the underlying sequences). You can use trim()
  to trim these ranges. See ?`trim,GenomicRanges-method` for more
  information.

Execution halted

This occurs in asifzubair/atacseeker:v8

arcolombo commented 8 years ago

is Circular, sounds like the left side is greater the right range.. , negative lengths....

asifzubair commented 8 years ago

Yup, however, not so worried about that because it is a warning for one of the scaffolds.

More concerned about this:

Error in coverage(x)/metadata(x)$totals : 
  non-numeric argument to binary operator
asifzubair commented 8 years ago

this has been fixed. plotRegion now works!