to run RSEM for 3 samples

[anitha-2211]

i need to generate the count table using 3 paired end samples such as leaf, stem and root. i used this command, but it is not running.
First i have created the index
./rsem-prepare-reference --bowtie2 transcript.fasta index_name
Second command to calculate the expression to generate count table
./rsem-calculate-expression --bowtie2 --paired-end -p 16 --no-bam-output
/home/altschul/Pavitra/proso_millet/leaf/paired_output.fastq /home/altschul/Pavitra/proso_millet/leaf/paired_output2.fastq
/home/altschul/Pavitra/proso_millet/root/paired_output.fastq /home/altschul/Pavitra/proso_millet/root/paired_output2.fastq
home/altschul/Pavitra/proso_millet/stem/paired_output.fastq /home/altschul/Pavitra/proso_millet/stem/paired_output2.fastq
proso_index /home/altschul/Pavitra/proso_millet/rnaspades/rsem_output
Invalid number of arguments!

[rbadmi]

Did you try running them separately? I mean just do the leaf first and then go to other tissues?