Does not look like an error. With that command line you just prepared the reference. Here the different usage of align_and_estimate_abundance.pl

## Just prepare the reference for alignment and abundance estimation
#
#    $0 --transcripts Trinity.fasta --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference
#
#   ## Run the alignment and abundance estimation (assumes reference has already been prepped, errors-out if prepped reference not located.)
#
#    $0 --transcripts Trinity.fasta --seqType fq --left reads_1.fq --right reads_2.fq --est_method RSEM --aln_method bowtie --trinity_mode --output_dir rsem_outdir
#
##  ## prep the reference and run the alignment/estimation
#
#    $0 --transcripts Trinity.fasta --seqType fq --left reads_1.fq --right reads_2.fq --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference --output_dir rsem_outdir
#
#   ## Use a samples.txt file:
#
#    $0 --transcripts Trinity.fasta --est_method RSEM --aln_method bowtie2 --prep_reference --trinity_mode --samples_file samples.txt --seqType fq  
#