In Sys.setlocale(“LC_MESSAGES”, “en_US.UTF-8”) :
OS reports request to set locale to “en_US.UTF-8” cannot be honored
Import genomic features from the file as a GRanges object … OK
Prepare the ‘metadata’ data frame … OK
Make the TxDb object … OK
‘select()’ returned 1:1 mapping between keys and columns
reading in files with read.delim (install ‘readr’ package for speed up)
1 reading in files with read.delim (install ‘readr’ package for speed up)
1 Error in tximport(txi_files, type = txtype, tx2gene = tx2gene, ignoreTxVersion = TRUE) :
all(c(abundanceCol, countsCol, lengthCol) %in% names(raw)) is not TRUE
Calls: get_deseq_dataset → tximport → stopifnot
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.
The error message above was generated running deseq2 on a salmon output that had previously been run without a problem. The only difference was the output was filtered for counts >5 in column 5 of the salmon quant output. The filter looks like it worked, the format looks the same.