Problem with MAFFT Multiple Sequence Alignment
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. :)))
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