Should I be able to create a tree with over 80,000 sequences? The dist.seqs command worked fine, and now clearcut appears to be running (my Mac’s energy usage is ~100% for Terminal). It’s been almost two days though. Should I just wait it out? Or is this too big of a task?
Doug
If it hasn’t crashed yet, it’s probably doable, it’s just a matter of how long it will take. Unfortunately, it’s hard to say how long…
Pat
Dear colleagues,
I am new to this form please be patient with me, I have generated a large sequences distance matrix using dist.seq, it took smote time to generate the file but eventually it did.
It took 12389 seconds to calculate the distances for 232994 sequences.
Now I am trying to use clearcut to make a tree (as Miseq SOP) as i am interested in phylogenetic diversity and unifrac commands for my 36 sample! I have been running clearcut command (mother 1.35) for the past 4 days on a ubuntu machine (0.5T RMA and 14T space). when do i give up? its still running. would such a large number of sequences crash clearcut?
mothur > clearcut(fasta=endo.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, DNA=T, version=t, verbose=t, neighbor=t, matrixout=myseed119_analysis.dist)
Clearcut Version: 1.0.9
PRNG SEED: 1450352028
Thanks
Feras
It probably won’t complete if you have a gigantic distance matrix. This is the type of application where phylogenetic methods fall apart. In the future, please start a new thread rather than tacking your question on to the end of a very old thread.
Pat