I have 30 individuals that have two samples each. I've had no problem running Cuffdiff between the individuals' samples, but I keep getting the "Loading reference annotation and inspecting maps and determining fragment length distributions" errors when running all 60 samples (30 samples for each condition) through Cuffdiff on my galaxy cloud instance.
Because I was running out of RAM on the public galaxy server, I transferred all of my accepted hits file onto a cloud instance along with my merged transcript file but the above error keeps popping up.
I've seen some posts that have a similar problem but I couldn't find a direct solution. I've also double check that all the files match up with the cuff merge dataset and that the same reference annotation was used during cufflinks and cuff merge. I hope I don't have to rerun tophat and cufflinks on my galaxy cloud instance but I'm starting to get desperate.
To identify what files were causing the errors I decided to split my 60 samples (30 indviduals) into two groups. Then, I re-ran cuff merge on both groups. After re-running cuffdiff on my new merged transcripts, the first group ran without any problems while the second group stopped prematurely with the same error expressed above. To further investigate I split up the last 15 individuals into 3 groups. But after running cuff merge and cuffdiff on these 3 groups they all completed with out any errors. Now I even more confused on what is happening...