Hi guys, I ran MSA with MAFFT (FFT-NS-i method with two cycles) in my university server, which has 31.3GB memory and 31.9GB swap memory. My input file has 8579 sequences (All human coronaviruses) [~253MB]. The job has running for 5 days already and suddenly the job has been killed not long ago (after I logged out from the server for a few mins). Here is the statement/program lines has appeared:
/usr/local/bin/mafft: line 2604: 25726 Killed "$prefix/dvdr" -W $minimumweight $bunkatsuopt -E $fixthreshold -s $unalignlevel $legacygapopt $mergearg $outnum -C $numthreadsit -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -Q $spfactor -h $aof -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy $scoreoutarg -K $nadd < pre > /dev/null 2>> "$progressfile"
I've been watching the status of the server when the MSA job is running and I realised MAFFT took a lot of memory space to run MSA (particularly this iterative refinement method). The used memory space can go as high as 97% (30.9G/31.3G). And today I saw the memory swap went high as well, the highest memory swap is 29-30+G/31.9G (I couldnt remember the specific number of I think is around this range).
I thought I accidentally killed the job before I detached the screen but I remembered clearly I didnt killed the job. If I killled the job the program lines above would not appeared. So I tried to search the cause of the job killed and I saw from a forum that people might it could be because of memory problem. I am not sure is it because of memory space issue. Hence, can anyone explain me why my job/process get killed?
Thank you in advanced for all the suggestions and explanations and I will appreciate all the responses. :)))
MAFFT online server (https://mafft.cbrc.jp/alignment/server/) is a very good option as an alternative.
Hi there, I have tried MAFFT online server but my sequence data are too big to run in MAFFT server. My job get killed when I tried in MAFFT server due to time restriction. MAFFT online server only allows users' MSA job to run for 24 hours. After 24 hours the server will automatically terminate your job. This is why I've been using my university's server due to time restriction by MAFFT server.
Hi, Why not try with this version (https://mafft.cbrc.jp/alignment/software/closelyrelatedviralgenomes.html). you can find some information here. Thank you.