Hi, I'm a new to learning DESeq,

I am having a similar problem that has been talked about here. This is the error:
Error in Ops.factor(a$V1, l[[1]]$V1) : 
  level sets of factors are different
In addition: Warning message:
In is.na(e1) | is.na(e2) :
  longer object length is not a multiple of shorter object length

This is the script I am using:
library("DESeq2")

files = c("merged_sample_2.bam_htseq_out.txt","merged_sample_11.bam_htseq_out.txt","merged_sample_20.bam_htseq_out.txt","merged_sample_3.bam_htseq_out.txt","merged_sample_12.bam_htseq_out.txt","merged_sample_21.bam_htseq_out.txt")

cond = c("GFP","GFP","GFP","DBM","DBM","DBM")

sTable = data.frame(sampleName = files, fileName = files, condition = cond)

dds <-DESeqDataSetFromHTSeqCount(sampleTable=sTable, directory = "/Volumes/cachannel/RNA_SEQ/Notch_RNASeq/in_silico_test/DESeq", design = ~condition)

I also tried running this code from the command line to filter the count files as seen in a different post:
cut -f merged_sample_2.bam_htseq_out.txt | sort | uniq -c
But got this error:
cut: [-cf] list: illegal list value

Any help would be appreciated. Thanks!

How were the htseq-count files generated? The error message (which is not clear and should be fixed) makes me think that the different files may have different gene IDs, which shouldn't be the case if you used the same GTF file for all the samples.