Hello,

Any one what is wrong with following message?

Thanks in advance for great help!

Best,

Yue

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
'select()' returned 1:many mapping between keys and columns



> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.1

The warning you got is

The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.

Which makes sense, given the GFF specification for this column:

Column 8: "phase"

    For features of type "CDS", the phase indicates where the next codon begins relative to the 5' end (where the 5' end of the CDS is relative to the strand of the CDS feature) of the current CDS feature. For clarification the 5' end for CDS features on the plus strand is the feature's start and and the 5' end for CDS features on the minus strand is the feature's end. The phase is one of the integers 0, 1, or 2, indicating the number of bases forward from the start of the current CDS feature the next codon begins. A phase of "0" indicates that a codon begins on the first nucleotide of the CDS feature (i.e. 0 bases forward), a phase of "1" indicates that the codon begins at the second nucleotide of this CDS feature and a phase of "2" indicates that the codon begins at the third nucleotide of this region. Note that ‘Phase’ in the context of a GFF3 CDS feature should not be confused with the similar concept of frame that is also a common concept in bioinformatics. Frame is generally calculated as a value for a given base relative to the start of the complete open reading frame (ORF) or the codon (e.g. modulo 3) while CDS phase describes the start of the next codon relative to a given CDS feature.

    The phase is REQUIRED for all CDS features.

If you have a stop codon, and the phase column has anything but NA, that makes no sense, given the definition of what is supposed to be there. So you got a warning saying that these non-NA values were ignored.