Error creating DESeq2 Data Set from HTSeq-Count

Question

[williamtmills]

I am trying to run DESeq2 using gene counts generated by HTSeq-Count.

I combine files for different conditions:

directory <- "~/GeneCountFiles/"

WT_Files <- c(
  "P0CTRS3.aligned.sam.genecount",
  "P0CTRS4.aligned.sam.genecount",
  "P0CTRS5.aligned.sam.genecount"
)

KO_Files <- c(
  "P0CTRS1.aligned.sam.genecount",
  "P0CTRS2.aligned.sam.genecount",
  "P0CTRS6.aligned.sam.genecount"
)

I then create the sample table:

sampleTable <- data.frame(
                        sampleName=c(WT_Files, KO_Files), 
                        fileName=c(WT_Files, KO_Files), 
                        genotype=c(rep("WT", length(WT_Files)), rep("KO", length(KO_Files))))

Then I try to create the data set for DESeq2:

library("DESeq2")

ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design = ~genotype)

However, this produces the error:

Error in read.table(file.path(directory, fn), fill = TRUE) : no lines available in input

Any ides why this is happening? I wasn't having any issues just a couple days ago.