Hi, I am Hao. I have an issue with the "getPromoterSeq" function from "GenomicFeatures" package.

I was trying to obtain potential promoter sequences for all genes in maize chromosome 1. I have the sequence file "Zea_mays.AGPv4.dna.chromosome.1.fa", and the total genome annotation file "Zea_mays.AGPv4.40.gff3".

I arbitrarily defined promoter region as 2,000 bp upstream from TSS and 500 bp downstream of TSS. The code I wrote is as follows.

library("Rsamtools")
FaFile=FaFile("Zea_mays.AGPv4.dna.chromosome.1.fa") #subject

library("GenomicRanges")

library("ape")
gffRangedData=read.gff("Zea_mays.AGPv4.40.gff3", na.strings = c(".", "?")) 
myGranges<-as(gffRangedData, "GRanges")   #query

library("GenomicFeatures")
Promoter=getPromoterSeq(myGranges,FaFile,upstream=2000, downstream=500)  

However, it returned me an error after using the "getPromoterSeq" function (see below). 

Error in value[[3L]](cond) :  record 1 (1:-1999-500) was truncated
  file: Zea_mays.AGPv4.dna.chromosome.1.fa
In addition: Warning message:
In .local(x, upstream, downstream, ...) : '*' ranges were treated as '+'

Below is the sessionInfo() output

> sessionInfo() 
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] GenomicFeatures_1.30.3 AnnotationDbi_1.40.0   Biobase_2.38.0         ape_5.1               
 [5] Rsamtools_1.30.0       Biostrings_2.46.0      XVector_0.18.0         GenomicRanges_1.30.3  
 [9] GenomeInfoDb_1.14.0    IRanges_2.12.0         S4Vectors_0.16.0       BiocGenerics_0.24.0   
[13] BiocInstaller_1.28.0  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18               compiler_3.4.4             prettyunits_1.0.2         
 [4] bitops_1.0-6               tools_3.4.4                zlibbioc_1.24.0           
 [7] progress_1.2.0             biomaRt_2.34.2             digest_0.6.16             
[10] bit_1.1-14                 RSQLite_2.1.1              memoise_1.1.0             
[13] nlme_3.1-131.1             lattice_0.20-35            pkgconfig_2.0.2           
[16] rlang_0.2.2                Matrix_1.2-12              DelayedArray_0.4.1        
[19] DBI_1.0.0                  rstudioapi_0.7             GenomeInfoDbData_1.0.0    
[22] rtracklayer_1.38.3         httr_1.3.1                 stringr_1.3.1             
[25] hms_0.4.2                  bit64_0.9-7                grid_3.4.4                
[28] R6_2.2.2                   XML_3.98-1.16              RMySQL_0.10.15            
[31] BiocParallel_1.12.0        magrittr_1.5               blob_1.1.1                
[34] matrixStats_0.54.0         GenomicAlignments_1.14.2   SummarizedExperiment_1.8.1
[37] assertthat_0.2.0           stringi_1.1.7              RCurl_1.95-4.11           
[40] crayon_1.3.4              

I was wondering if anyone could help me out? Many thanks!