[BioC] Oryza sativa problem

[abhishek singh chauhan [guest]]

While running this command i will get this error.


> count.table <- easyRNASeq(system.file(
+ "data",
+ package="RnaSeqTutorial"),
+ organism="Osativa", 
+ chr.map=chr.map,
+ chr.sizes=chr.size,
+ annotationMethod="gtf",
+ annotationFile=system.file(
+ "data",
+ "Oryza.gtf",
+ package="RnaSeqTutorial"),
+ count="exons",
+ filenames=c("accepted_hits_sort.bam"))
Checking arguments... 
Fetching annotations... 
Read 420833 records
Summarizing counts... 
Processing accepted_hits_sort.bam 
Updating the read length information. 
The reads have been trimmed. 
Minimum length of 82 bp. 
Maximum length of 83 bp. 
Error in if (any(unlist(start(aln.info$rng.list), use.names = FALSE) >  : 
  missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In easyRNASeq(system.file("data", package = "RnaSeqTutorial"), organism = "Osativa",  :
  You enforce UCSC chromosome conventions, however the provided chromosome size list is not compliant. Correcting it.
2: In .convertToUCSC(names(chrSize(obj)), organismName(obj), chr.map) :
  No function implemented to convert the names for the organism: Osativa.
Available ones so far exists for: Dmelanogaster, Hsapiens, Mmusculus, Rnorvegicus.
If you need to provide your own mapping, use the 'custom' argument.
3: In easyRNASeq(system.file("data", package = "RnaSeqTutorial"), organism = "Osativa",  :
  There are 59177 features/exons defined in your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want?
4: In easyRNASeq(system.file("data", package = "RnaSeqTutorial"), organism = "Osativa",  :
  You enforce UCSC chromosome conventions, however the provided annotation is not compliant. Correcting it.
5: In .convertToUCSC(names(genomicAnnotation(obj)), organismName(obj),  :
  No function implemented to convert the names for the organism: Osativa.
Available ones so far exists for: Dmelanogaster, Hsapiens, Mmusculus, Rnorvegicus.
If you need to provide your own mapping, use the 'custom' argument.
6: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter,  :
  You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it.
7: In .convertToUCSC(names(aln.info$rng.list), organismName(obj), chr.map) :
  No function implemented to convert the names for the organism: Osativa.
Available ones so far exists for: Dmelanogaster, Hsapiens, Mmusculus, Rnorvegicus.
If you need to provide your own mapping, use the 'custom' argument.
8: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter,  :
  The chromosome(s): 1, 10, 11, 12, 2, 3, 4, 5, 6, 7, 8, 9 is (are) not present in the provided 'chr.sizes' argument


 -- output of sessionInfo(): 

> count.table <- easyRNASeq(system.file(
+ "data",
+ package="RnaSeqTutorial"),
+ organism="Osativa", 
+ chr.map=chr.map,
+ chr.sizes=chr.size,
+ annotationMethod="gtf",
+ annotationFile=system.file(
+ "data",
+ "Oryza.gtf",
+ package="RnaSeqTutorial"),
+ count="exons",
+ filenames=c("accepted_hits_sort.bam"))
Checking arguments... 
Fetching annotations... 
Read 420833 records
Summarizing counts... 
Processing accepted_hits_sort.bam 
Updating the read length information. 
The reads have been trimmed. 
Minimum length of 82 bp. 
Maximum length of 83 bp. 
Error in if (any(unlist(start(aln.info$rng.list), use.names = FALSE) >  : 
  missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In easyRNASeq(system.file("data", package = "RnaSeqTutorial"), organism = "Osativa",  :
  You enforce UCSC chromosome conventions, however the provided chromosome size list is not compliant. Correcting it.
2: In .convertToUCSC(names(chrSize(obj)), organismName(obj), chr.map) :
  No function implemented to convert the names for the organism: Osativa.
Available ones so far exists for: Dmelanogaster, Hsapiens, Mmusculus, Rnorvegicus.
If you need to provide your own mapping, use the 'custom' argument.
3: In easyRNASeq(system.file("data", package = "RnaSeqTutorial"), organism = "Osativa",  :
  There are 59177 features/exons defined in your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want?
4: In easyRNASeq(system.file("data", package = "RnaSeqTutorial"), organism = "Osativa",  :
  You enforce UCSC chromosome conventions, however the provided annotation is not compliant. Correcting it.
5: In .convertToUCSC(names(genomicAnnotation(obj)), organismName(obj),  :
  No function implemented to convert the names for the organism: Osativa.
Available ones so far exists for: Dmelanogaster, Hsapiens, Mmusculus, Rnorvegicus.
If you need to provide your own mapping, use the 'custom' argument.
6: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter,  :
  You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it.
7: In .convertToUCSC(names(aln.info$rng.list), organismName(obj), chr.map) :
  No function implemented to convert the names for the organism: Osativa.
Available ones so far exists for: Dmelanogaster, Hsapiens, Mmusculus, Rnorvegicus.
If you need to provide your own mapping, use the 'custom' argument.
8: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter,  :
  The chromosome(s): 1, 10, 11, 12, 2, 3, 4, 5, 6, 7, 8, 9 is (are) not present in the provided 'chr.sizes' argument


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