I'm trying to run ChIPSeeker with annotation files from Ensembl, but it keep giving me an error.

I have changed the seqlevels to "UCSC" ( see below), but when running this command

peakAnno1 <- annotatePeak(peak = peak1, tssRegion=c(-3000, 3000), TxDb = edb)

I get the error

>> preparing features information...         2020-04-06 12:58:26 
>> identifying nearest features...       2020-04-06 12:58:26 
>> calculating distance from peak to TSS...  2020-04-06 12:58:28 
>> assigning genomic annotation...       2020-04-06 12:58:28 
Error in `[.data.frame`(nearestFeatures.df, , cn) : 
  undefined columns selectedError in `[.data.frame`(nearestFeatures.df, , cn) : undefined columns selected

I can't figure out which columns are looked for to debug the problem.

Any ideas, why this is happening? I habe also tried with and without the annoDb = "org.Mm.eg.db" or annoDb = "EnsDb.Mmusculus.v79"

thanks

Assa

> peak1
GRanges object with 202315 ranges and 6 metadata columns:
           seqnames              ranges strand |                      V4        V5       V6        V7        V8        V9
              <Rle>           <IRanges>  <Rle> |                <factor> <integer> <factor> <numeric> <numeric> <numeric>
       [1]     chr1     3261236-3261429      * |      H3K4m3_WK31_peak_1        10        .   2.71368   2.82763   1.05939
       [2]     chr1     3264207-3264630      * |      H3K4m3_WK31_peak_2        55        .    5.8844   8.00663   5.58589
       [3]     chr1     3339728-3339940      * |      H3K4m3_WK31_peak_3         0        .   1.87219   1.68288   0.08676
       [4]     chr1     3369422-3369611      * |      H3K4m3_WK31_peak_4        11        .   3.24958   2.88762   1.11099
       [5]     chr1     3469328-3469531      * |      H3K4m3_WK31_peak_5        21        .   3.66036   4.09408   2.14879
       ...      ...                 ...    ... .                     ...       ...      ...       ...       ...       ...
  [202311]     chrX 167635685-167636864      * | H3K4m3_WK31_peak_202311        28        .   3.99902   4.92286   2.89243
  [202312]     chrX 167641667-167642491      * | H3K4m3_WK31_peak_202312        17        .   3.34516   3.66866   1.78698
  [202313]     chrX 167647254-167647450      * | H3K4m3_WK31_peak_202313        10        .   3.03725   2.84692   1.07598
  [202314]     chrX 167648493-167650286      * | H3K4m3_WK31_peak_202314        10        .   2.93389    2.7888   1.03137
  [202315]     chrX 167651479-167651741      * | H3K4m3_WK31_peak_202315       106        .   8.56011  13.63289  10.61471
  -------
  seqinfo: 21 sequences from an unspecified genome; no seqlengths
> seqlevels(edb)
 [1] "chr1"                      "chr10"                     "chr11"                     "chr12"                    
 [5] "chr13"                     "chr14"                     "chr15"                     "chr16"                    
 [9] "chr17"                     "chr18"                     "chr19"                     "chr2"                     
[13] "chr3"                      "chr4"                      "chr5"                      "chr6"                     
[17] "chr7"                      "chr8"                      "chr9"                      "CHR_MG132_PATCH"          
[21] "CHR_MG153_PATCH"           "CHR_MG184_PATCH"           "CHR_MG3829_PATCH"          "CHR_MG3833_PATCH"         
[25] "CHR_MG4136_PATCH"          "CHR_MG4151_PATCH"          "CHR_MG4180_PATCH"          "CHR_MG4209_PATCH"         
[29] "CHR_MG4211_PATCH"          "CHR_MG4212_PATCH"          "CHR_MG4213_PATCH"          "CHR_MG4214_PATCH"         
[33] "CHR_MG4222_MG3908_PATCH"   "CHR_MG4237_PATCH"          "CHR_MMCHR1_CHORI29_IDD5_1" "GL456210.1"               
[37] "GL456211.1"                "GL456212.1"                "GL456216.1"                "GL456219.1"               
[41] "GL456221.1"                "GL456233.1"                "GL456239.1"                "GL456350.1"               
[45] "GL456354.1"                "GL456372.1"                "GL456381.1"                "GL456385.1"               
[49] "JH584292.1"                "JH584293.1"                "JH584294.1"                "JH584295.1"               
[53] "JH584296.1"                "JH584297.1"                "JH584298.1"                "JH584299.1"               
[57] "JH584303.1"                "JH584304.1"                "chrM"                      "chrX"                     
[61] "chrY"