I am using RNA STAR in usegalaxy.org to align some sequences to Arabidopsis thaliana genome to get the reads per gene (text file) for downstream analysis. The genome file and annotation file are fine as they worked for other datasets I analysed before. I used the unzipped fastq-dump file for the raw data. However, while aligning sequences using exactly the same parameters this time, the mapped.bam, spliced junctions.bed and log files finished running within one day but the reads per gene file does not finish running for about 8 days. I clicked to see the data in the reads per gene file and it seems like all the data are already aligned, just that I cannot download it.
Does anyone experienced this and know what is the problem?