rsem calculate expression error

[pablanedo]

Hello ,

I am trying to run an analysis on rsem-calculate-expression but keep getting an error that says invalid number of arguments. The command below is what I am inputting:

RSEM-1.3.3/rsem-calculate-expression --bowtie2 -p 30 --paired-end \ trimmed/CON1_1.tp.fq.gz\ trimmed/ CON1_2.tp.fq.gz\ Human_genome.seq\ CON1

Also, I used the rsem-prepare-reference to prepare human genome from genome downloaded from ensembl RSEM-1.3.3/rsem-prepare-reference --gtf Homo_sapiens.GRCh38.83.gtf \ --bowtie2 \ --bowtie2-path ./bowtie2-2.4.5-macos-x86_64 \ Homo_sapiens.GRCh38.dna.primary_assembly.fa \ Human_genome

I obtained several files from this analysis and using the Human_genome.seq, is this the correct one?