Hi, while trying to make TxDb from gff file, I received the following warning message. Should I be concerned? How to interpret the warnings? Many thanks for your help!

Best regards,

Julie

gtffile <- file.path(dir,"ENSEMBLchrExt.v14.no.rRNA.gtf")
(ensemblchrExt_v14_no_rRNA_txdb <- makeTxDbFromGFF(gtffile, format="gtf", circ_seqs =character()))

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: /s4s/s4s_nathan_lawson/SC3primeSeq/ENSEMBLchrExt.v14.no.rRNA.gtf
# Organism: NA
# Taxonomy ID: NA
# miRBase build ID: NA
# Genome: NA
# transcript_nrow: 54275
# exon_nrow: 333697
# cds_nrow: 271232
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2016-11-10 13:59:09 -0500 (Thu, 10 Nov 2016)
# GenomicFeatures version at creation time: 1.26.0
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
Warning messages:
1: In .reject_transcripts(bad_tx, because) :
  The following transcripts were rejected because they have CDSs that
  cannot be mapped to an exon: ENSDART00000000102, ENSDART00000000804,
  ENSDART00000002299, ENSDART00000002571, ENSDART00000002856,
  ENSDART00000002922, ENSDART00000002949, ENSDART00000003690,
  ENSDART00000004209, ENSDART00000004721, ENSDART00000005195,
  ENSDART00000005499, ENSDART00000005740, ENSDART00000007064,
  ENSDART00000007247, ENSDART00000007914, ENSDART00000008554,
  ENSDART00000009363, ENSDART00000009443, ENSDART00000009755,
  ENSDART00000012507, ENSDART00000012551, ENSDART00000013534,
  ENSDART00000014528, ENSDART00000014877, ENSDART00000016019,
  ENSDART00000016183, ENSDART00000016582, ENSDART00000016753,
  ENSDART00000018425, ENSDART00000019006, ENSDART00000019992,
  ENSDART00000020040, ENSDART00000020116, ENSDART00000020234,
  ENSDART00000020765, ENSDART00000021469, ENSDART00000021977,
  ENSDART00000022349, ENSDART00000023039, ENSDART00000024009,
  ENSDART00000024593, ENSDART00000024846, ENSDART000000 [... truncated]
2: In .reject_transcripts(bad_tx, because) :
  The following transcripts were rejected because they have stop codons
  that cannot be mapped to an exon: ENSDART00000000102,
  ENSDART00000000804, ENSDART00000002299, ENSDART00000002571,
  ENSDART00000002856, ENSDART00000002922, ENSDART00000002949,
  ENSDART00000004209, ENSDART00000004721, ENSDART00000005195,
  ENSDART00000005499, ENSDART00000005740, ENSDART00000007064,
  ENSDART00000007247, ENSDART00000007914, ENSDART00000008554,
  ENSDART00000009363, ENSDART00000009443, ENSDART00000009755,
  ENSDART00000012507, ENSDART00000012551, ENSDART00000013534,
  ENSDART00000014528, ENSDART00000016019, ENSDART00000016183,
  ENSDART00000016582, ENSDART00000016753, ENSDART00000018425,
  ENSDART00000019006, ENSDART00000019992, ENSDART00000020040,
  ENSDART00000020116, ENSDART00000020234, ENSDART00000020765,
  ENSDART00000021469, ENSDART00000021977, ENSDART00000023039,
  ENSDART00000024009, ENSDART00000024593, ENSDART00000024846,
  ENSDART00000024861, ENSDART00000024967, ENSDART00000024992,
  ENSD [... truncated]

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.8 (Santiago)

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] GenomicFeatures_1.26.0 AnnotationDbi_1.36.0   Biobase_2.34.0        
[4] GenomicRanges_1.26.1   GenomeInfoDb_1.10.0    IRanges_2.8.0         
[7] S4Vectors_0.12.0       BiocGenerics_0.20.0    Rsubread_1.24.0       

loaded via a namespace (and not attached):
 [1] XVector_0.14.0             zlibbioc_1.20.0           
 [3] GenomicAlignments_1.10.0   BiocParallel_1.8.0        
 [5] lattice_0.20-34            tools_3.3.1               
 [7] SummarizedExperiment_1.4.0 grid_3.3.1                
 [9] DBI_0.5-1                  Matrix_1.2-7.1            
[11] rtracklayer_1.34.0         bitops_1.0-6              
[13] RCurl_1.95-4.8             biomaRt_2.30.0            
[15] RSQLite_1.0.0              Biostrings_2.42.0         
[17] Rsamtools_1.26.0           XML_3.98-1.4 

As it looks like the GTF you're using is from Ensembl - eventually you could also give a shot at the ensembldb package and create an EnsDb database/package instead (same functionality as the TxDb, but tables and annotations tailored for Ensembl annotations).

library(ensembldb)
## First create the SQLite database
db <- ensDbFromGtf(gtf = gtffile)
## Load that database and use it
edb <- EnsDb(db)
edb

You can use the same methods than with TxDbs. Have also a look at the ensembldb vignette for some more informations and capabilities.

cheers, jo