I have the latest MacBook Pro with the following specs:
Processor: 2.9Ghz Intel Core i7
Memory: 16GB 2133 MHz LPDDR3
When I run the following command inside MacQIIME:
pick_closed_reference_otus.py -i combined_seqs.fna -o RESULTS -r gg_13_5.fasta -p params.txt -t gg_13_5_taxonomy.txt --parallel --jobs_to_start=2
... my Mac runs out of application memory and freezes.
The params.txt file contains the following:
My combined_seqs.fna file consists of 6,153,481 sequences, but I have no trouble when running the exact same against Silva (https://www.arb-silva.de/
The Greengenes files (gg_13_5.fasta and gg_13_5_taxonomy.txt) were downloaded from http://greengenes.secondgenome.com/downloads/database/13_5
How can I prevent this from happening? Should I split the combined_seqs.fna file somehow? Should I change any settings in my Mac? Am
I using the correct Greengenes files?
I'd really appreciate if someone could shed some light! Many thanks!