[root@e4be531692a7  22:34:32 /work/my_rnaseq/5.deg.]# Rscript $scriptdir/deseq_analysis.r -i $workdir/4.expression/all_gene_count.tsv -g J1_vs_J2.compare.txt  -k $workdir/4.expression/all_gene_fpkm.tsv -r J1 --fdr 0.05 --fc 2 -p J1_vs_J2

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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,  :

  duplicate 'row.names' are not allowed

Calls: read.delim -> read.table

Execution halted