When I run cluster.split(), our server has 8 processors, and I use 8 processors. Before this step. All the data run takes 24 hours. When came to this step, it has been run for 48 hours, and the system broke. Then I ran it again, from 0.dist to 4.dist not more than 1 hour, but the 5.dist is running very slowly.
Is there anything wrong with my data running?
Thanks.
Here is my code used:
cluster.split(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table, taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy, splitmethod=classify, taxlevel=4, cutoff=0.03,processors=8)
You might also try taxlevel=5 or =6. Would also be good to know what your sequencing error rate is and how much RAM you have access to. What version of mothur are you using?
Pat
Hi. Dr. Schloss,
I am using a mothur 1.39.5. I am wondering is it rare or not for this kind of calculation speed?
My “stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.5.dist” file now is 7.9G now, and it is still changing larger. I am afraid.
Others are:
4.2G Oct 5 11:26 full.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.5.dist3411.temp
8.2G Oct 5 11:26 full.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.5.dist3412.temp
6.7G Oct 5 11:26 full.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.5.dist3413.temp
1.5G Oct 5 11:26 full.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.5.dist3414.temp
781M Oct 5 11:25 full.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.5.dist3415.temp
1016M Oct 5 11:26 full.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.5.dist3416.temp
1.5G Oct 5 11:26 full.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.5.dist3417.temp