Entering edit mode
4.2 years ago
hafiz.talhamalik
▴
350
I am using maker tool for annotation of a plant genome (non-model specie). I generated the de-novo assembly and now I doing it's annotation. It's been 3 days now and annotation is not completed yet. fasta file size was around 450MB. as per my thinking it shouldn't be taking that long. Anyone has the idea how much time it takes ?? why its taking that long ?
Running time of MAKER is mostly related to the number of evidence sequence (protein / transcript) you use. Big dataset will be long... The repeat masking is quite consuming too. Hon many cpu do you use? With 80cpu it might run 48hours...
for blast I used 10cpus.
No MPI? So then yes could take easily a week... even more
Running time of MAKER is mostly related to the number of evidence sequence (protein / transcript) you use. Big dataset will be long... The repeat masking is quite consuming too. Hon many cpu do you use? With 80cpu it might run 48hours...