Hi. I created a workflow to map IGA reads using bowtie and generate a pileup at the end. The workflow is FASTQ Groomer -> Map with Bowtie for Illumina -> SAM-to-BAM -> Generate pileup. I ran the workflow successfully using the built-in mm9 index as reference for both bowtie and the pileup generation. Then I changed the workflow to use a reference file I uploaded (fasta format) and now I get an error on the pileup generation step:
An error occurred running this job: /The output file is empty. Your input file may have had no matches, or there may be an error with your input file or settings./
The prior SAM-to-BAM step shows a sizeable BAM file being generated. So I am wondering if the Generate pileup tool requires the reference in a special format.
V. Patel Dept. of Human Genetics Emory University School of Medicine