Hi everyone,

I am using exomePeak (v.2.13.2) to call peaks from chip-seq data. This is the command I am using:

result <- exomepeak(GENE_ANNO_GTF=gtf, IP_BAM=f2, INPUT_BAM=f1)

But it fails, the error message is:

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:many mapping between keys and columns
[1] "Divide transcriptome intochr-gene-batch sections ..."
[1] "Get Reads Count ..."
[1] "This step may take a few hours ..."
[1] "100 %"
[1] "Get all the peaks ..."
Error in .subset2(x, i, exact = exact) : subscript out of bounds
Calls: exomepeak ... .report.peak.based.on.result -> [[ -> [[.data.frame -> <Anonymous>
Execution halted

The sessionInfo() output:

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /miniconda/lib/R/lib/libRblas.so
LAPACK: /miniconda/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] exomePeak_2.13.2           GenomicAlignments_1.14.1
 [3] SummarizedExperiment_1.8.0 DelayedArray_0.4.1
 [5] matrixStats_0.53.1         rtracklayer_1.38.3
 [7] GenomicFeatures_1.28.5     AnnotationDbi_1.40.0
 [9] Biobase_2.38.0             Rsamtools_1.30.0
[11] Biostrings_2.46.0          XVector_0.18.0
[13] GenomicRanges_1.30.3       GenomeInfoDb_1.14.0
[15] IRanges_2.12.0             S4Vectors_0.16.0
[17] BiocGenerics_0.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17           compiler_3.4.1         prettyunits_1.0.2
 [4] bitops_1.0-6           tools_3.4.1            zlibbioc_1.24.0
 [7] progress_1.2.0         biomaRt_2.34.2         digest_0.6.15
[10] bit_1.1-12             lattice_0.20-34        RSQLite_2.0
[13] memoise_1.1.0          Matrix_1.2-14          DBI_1.0.0
[16] GenomeInfoDbData_1.0.0 stringr_1.3.1          httr_1.3.1
[19] hms_0.3                grid_3.4.1             bit64_0.9-5
[22] R6_2.2.2               XML_3.98-1.11          BiocParallel_1.12.0
[25] blob_1.1.1             magrittr_1.5           assertthat_0.2.0
[28] stringi_1.2.3          RCurl_1.95-4.11        crayon_1.3.4

Here is some lines of my GTF file:

##gff-version 2

##source-version rtracklayer 1.40.3

##date 2018-07-24

NC_007605.1 RefSeq  exon    59  272 .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "28"

NC_007605.1 RefSeq  exon    360 458 .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "29"

NC_007605.1 RefSeq  exon    540 788 .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "30"

NC_007605.1 RefSeq  exon    871 951 .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "31"

NC_007605.1 RefSeq  exon    1026    1196    .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "32"

NC_007605.1 RefSeq  exon    1280    1495    .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "33"

NC_007605.1 RefSeq  exon    1574    1680    .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "34"

What is the problem and how can I fix it? Thanks!