RepeatModeler to identify repeats de novo in some genomic sequences. However, I'm running into an error I don't quite understand. Here is the last bit of the terminal output.
100% completed, 0:0:0 (hh:mm:ss) est. time remaining. - Comparing batch-(85 of 86) to database: Converted 1 GIs 100% completed, 0:0:0 (hh:mm:ss) est. time remaining. Comparison Time: 0:8:7 Elapsed Time, 26954 HSPs Collected - RECON: Running imagespread.. RECON Elapsed: 0:0:0 Elapsed Time - RECON: Running initial definition of elements ( eledef ).. RECON Elapsed: 0:0:1 Elapsed Time - RECON: Running re-definition of elements ( eleredef ).. RECON Elapsed: 0:0:1 Elapsed Time - RECON: Running re-definition of edges ( edgeredef ).. edgeredef failed. Exit code 768 Command exited with non-zero status 2 1489.43user 3.94system 12:16.75elapsed 202%CPU (0avgtext+0avgdata 1461360maxresident)k 0inputs+135472outputs (0major+2254814minor)pagefaults 0swaps
It looks like RepeatModeler is failing shortly after it calls RECON, which in turn calls a few programs itself.. I've never used RECON before and I'm not sure what the
edgeredef program does, but it is failing. RECON successfully calls some other programs that seem to work fine, so I don't really know what the problem could be. Any ideas?
By the way, these are the commands I used to run
$ BuildDatabase -name 79BACs.fas 79BACs.fas $ nohup time RepeatModeler -database 79BACs.fas > out.txt 2>&1 &