Rscript $scriptdir/deseq_analysis.r -i $workdir/4.expression/all_gene_count.tsv -g S3_vs_S4.compare.txt  -k $workdir/4.expression/all_gene_fpkm.tsv -r S3 --fdr 0.01 --fc 2 -p S3_vs_S4

Loading required package: ggplot2

Loading required package: edgeR

Loading required package: limma

[1] "abstract_factors is start"

[1] "abstract_factors is over"

[1] "read count data ..."

Error in read.table(file = file, header = header, sep = sep, quote = quote,  :

  missing values in 'row.names' are not allowed

Calls: read.delim -> read.table

Execution halted