| Additional Information | I’ve used MEGA since about 4, and in the past few months I’ve moved to 11 having used 7 and X for years.
I’ve previously in X and 7 run trees of 800+ sequences each of 6,000 amino acyl residues or of 2,000 nt all on the same machine I’m on right now which has 8 cores at 3.4 GHz and >64Gb RAM and runs Windows 10 64 bit with all updates up to date. Try as I might, I CANNOT run a tree in MEGA 11 with bootstrapping. If I run an ML tree (GTR+G+I) sans replicates, it takes about 15 mins to draw (790 sequences, 1,500 nt, partial deletion, based on a MUSCLE alignment and model picked based on lowest BIC as a very high diversity dataset) which is VERY long compared to MEGA 7 drawing the same trees. The tree LOOKS fine. I then tried to run it with 2,250 replicates (not enough - needs 20,000 for this size dataset obviously but as it was having issues I decided to run a small number). It runs totally fine, 1 rep per 4 mins (which is far slower than it should be on 3 threads - MEGA 7 was faster!) and gets to about 30 and just stops. It doesn’t crash. It just stops. If I go into Task Manager I can see the CPU and RAM use are totally stable and don’t move at all over 1h indicating the software is doing nothing - and is using about 30% of CPU (which is at 33% capacity in toto) and about 2Gb RAM - plenty of disc space and SWAP file space too - no reason for this to hang. FYI, MEGA_64.exe is set on High Priority and I’ve affinitied it in Windows to 3 specific cores that nothing else uses - precisely as I always did in MEGA 7 and MEGA X. I’ve had this same issue with 3-4 datasets now, ranging from 50 sequences of 10,000 aa to 800 sequences of 1,500 nt - things that have run on MEGA 7 and MEGA X sans issues. I’ve had a colleague try it on MEGA 11 on his PC and he had the same issues and reported he has loads of issues with MEGA 11 and doesn’t use it.
I’m currently trying to run the same analysis in MEGA 7 which is running slower than I think it should but my PC hasn’t changed and nothing is using gallons of Ram/CPU. Surely having MEGA 7, MEGA X and MEGA 11 installed on the same device isn’t causing issues….?
Any help much appreciated - this work is really urgent as I’m trying to meet a revision deadline and tearing my hair out!!!
Thanks
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ABC subG (WBC).meg (135,285 bytes) 1969-12-31 17:33
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