Hi all,

Our RNA-seq pipeline uses GOseq, and we are thankful to the authors for
offering this great tools.

GOseq crashed on us today on C. elegans data with the error":

 "Couldn't grab GO categories automatically.  Please manually specify."

The workaround is to use the non-native mechanism.

After investigating, the error is thrown after the function getgo() cannot
reliably identify the org package associated to the Ce6 genome.There is a
collision with the yeast org package.

So for fun I listed all other genomes for which that would not work:

library(goseq,quietly = TRUE)
genomes = sort(supportedGenomes()$db)
.ORG_PACKAGES = goseq:::.ORG_PACKAGES

supported = sapply(genomes,function(genome)
{
    orgstring = as.character(.ORG_PACKAGES[grep(gsub("[0-9]+", "", genome),
names(.ORG_PACKAGES), ignore.case = TRUE)])
       if (length(orgstring) != 1) {
    #stop("Couldn't grab GO categories automatically.  Please manually
specify.")
    return(FALSE)
       }else{
    return(TRUE)
    }
})
print(names(supported[!supported]))


which prints:


  [1] "ailMel1" "allMis1" "anoCar1" "anoCar2" "apiMel1" "apiMel2" "aplCal1"

  [8] "braFlo1" "caeJap1" "caePb1"  "caePb2"  "caeRem2" "caeRem3" "calJac1"

 [15] "calJac3" "cavPor3" "cb1"     "cb3"     "ce10"    "ce2"     "ce4"

 [22] "ce6"     "cerSim1" "choHof1" "chrPic1" "ci1"     "ci2"     "dasNov3"

 [29] "dipOrd1" "dp2"     "dp3"     "droAna1" "droAna2" "droEre1" "droGri1"

 [36] "droMoj1" "droMoj2" "droPer1" "droSec1" "droSim1" "droVir1" "droVir2"

 [43] "droYak1" "droYak2" "echTel1" "echTel2" "equCab1" "equCab2" "eriEur1"

 [50] "felCat3" "felCat4" "felCat5" "fr1"     "fr2"     "fr3"     "gadMor1"

 [57] "gasAcu1" "geoFor1" "gorGor3" "hetGla1" "hetGla2" "latCha1" "loxAfr3"

 [64] "macEug2" "melGal1" "melUnd1" "micMur1" "monDom1" "monDom4" "monDom5"

 [71] "musFur1" "myoLuc2" "nomLeu1" "nomLeu2" "nomLeu3" "ochPri2" "oreNil2"

 [78] "ornAna1" "oryCun2" "oryLat2" "otoGar3" "oviAri1" "oviAri3" "papAnu2"

 [85] "papHam1" "petMar1" "petMar2" "ponAbe2" "priPac1" "proCap1" "pteVam1"

 [92] "saiBol1" "sarHar1" "sorAra1" "speTri2" "strPur1" "strPur2" "susScr2"

 [99] "susScr3" "taeGut1" "tarSyr1" "tetNig1" "tetNig2" "triMan1" "tupBel1"

[106] "turTru2" "vicPac1" "vicPac2"


I just thought it was odd for the package not to work out of the box for
the model organism C. elegans. It also wouldn't work for pig, and maybe
more.

Thank you!

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