Hi - I’m working with a data set of ~3.5 million contigs, using 40 processors, mothur v1.39.5, and the new v128 reference files (thanks Pat!). Everything was fine until I ran this command…
mothur > screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table, summary=stability.trim.contigs.good.unique.summary, start=1, end=16570, processors=40)
Mothur reported back…
Using 40 processors
A summary file was generated relatively quickly, but the command never completed (It was running for ~120 hours). Using htop I could see that mothur was only running on one processor and that there were plenty of additional processors available (but unused). The logfile never updated until I quit the command and the other expected files were never generated.
I’m running in interactive mode on our institutional cluster so I don’t think it’s a case of not having enough computing resources. Additionally, I’ve made it past this step with a data set of about half as many contigs, albeit on an earlier version of mothur (~August 2016).