I see that you have stopped answering any of the questions here for ~9 months. I am hoping you can do something here. Thanks in advance.
I have spent a lot of time trying to solve this problem but no luck. There is very little documentation about this function/program so I cannot seem to solve this myself.
When I run the following command, the run starts for many hours (5-15) and then aborts, but produces nothing other than "starting" in the error file:
Hi Everyone,
I see that you have stopped answering any of the questions here for ~9 months. I am hoping you can do something here. Thanks in advance.
I have spent a lot of time trying to solve this problem but no luck. There is very little documentation about this function/program so I cannot seem to solve this myself.
When I run the following command, the run starts for many hours (5-15) and then aborts, but produces nothing other than "starting" in the error file:
./Chromosemble -t Thamnophis_elegans-GCA_009769535.1-unmasked.fa -q Pantherophis-obs.fa -n 25 -s 1 -o PANTH_Chromo_NEW
.... Potential targets: 49293 Downsize to 292 MAIN: Targets retrieved: 292 MAIN: STATUS: iteration, slaves_processed, new_matches, slave_to_match_relation, targets_needed, targets_collected MAIN: STATUS: 112, 145, 161861, 1116.28, 292, 292, 2020/12/23 14:26:24 MAIN: starting iteration 113 WORKQUEUE: matches collected. FW: 59294 REV: 53738 MAIN: 113032 new matches collected MAIN: Running the chaining step... Matches before collapse: 9324374 Matches after collapse: 9305825 MAIN: running coverage tracker MAIN: coverage tracker: +4125929 -1792009 MAIN: DynProg... Chaining (inline)... Filling out repeat lists... Dynprog'ing...
ERROR!!! See log file for more error messages. ABORTING!