I’m trying to make a biom file for use in PICRUSt, but make.biom stops working and I get a notification that my 16GB RAM is all being used by mothur. I don’t get any output written to my file at all.
I’m using greengenes version 5 taxnomy along with the mapping file and my cons.tax file at 0.03. None of the files are extremely large. But the computer reports the virtual memory as ~80 GB.
What can I do to fix this?
Many thanks in advance!
It sounds like mothur is getting hung up somewhere. Can you post the version and command you are running?
Hello,
Thanks very much for the reply! I’m using mothur v.1.35.1 and the command is as follows:
make.biom(constaxonomy=/Users/x/2.an.unique_list.0.03.cons.pick.taxonomy, picrust=/Users/x/Downloads/GG_13_5_otuMapTable 2/97_otu_map.txt, reftaxonomy=/Users/x/Downloads/Gg_13_5_99.taxonomy/gg_13_5_99.gg.tax, shared=/Users/x/2.pick.shared, label=0.03)
I’ve also tried with the mothurGUI (same version of mothur v.1.35.1)
Edit:
Just tried with the newest version (1.36.1) and it has the same problem.
Could you send your log file and input files to mothur.bugs@gmail.com?