I'm attempting RNA-seq data analysis on Vibrio cholerae samples, at galaxy main https://main.g2.bx.psu.edu/.

I was able to align transcripts using Ion Torrent's TMAP aligner. I uploaded the BAM files and used the cufflinks tool, which gave me FPKM scores for various transcripts. Now I want to extract the relevant gene_id for each mapped transcript using a reference genome. I tried using CuffCompare for this purpose using a reference file from the UCSC archaea database or using a FASTA file from history. In either case, cuffcompare gives me an error. 

Error1: (When using a reference genome from the UCSC archaea database)

 An error occurred running this job:cuffcompare v2.0.2 (3522) No sequence data found for dbkey vibrChol1, so sequence data cannot be used. cp: cannot stat `/galaxy/main_pool/pool4/tmp/job_working_directory/004/846/4846005/cc_output.input1.refmap': No such file or directory cp: cannot stat `

Error 2: (When using a reference genome from history)