# First process raw reads, remove humans reads and generate taxonomic and mOTU profiles

# This code is part of the MOCAT analysis pipeline
# Code is (c) Copyright EMBL and BGI, 2012-2013
# This code is released under GNU GPL v3.

[command] -rtf
[command] -s hg19 -r reads.processed -identity 90 -screened_files
[command] -s mOTU.v1.padded -r hg19 -cpus 4 -identity 97 -extracted_files -config screen_soap_max_mm=5
[command] -f mOTU.v1.padded -r hg19 -identity 97 -config filter_psort_buffer=2G -memory 5G
[command] -s RefMG.v1.padded -r screened.hg19.on.mOTU.v1.padded -e -cpus 4 identity 97 -config screen_soap_max_mm=5
[command] -f RefMG.v1.padded -r screened.hg19.on.mOTU.v1.padded -e -identity 97 -config filter_psort_buffer=2G -memory 5G
[command] -p mOTU.v1.padded -r hg19 -mode mOTU -identity 97 -memory 3G
[command] -p RefMG.v1.padded -r screened.hg19.on.mOTU.v1.padded -e -identity 97 -mode RefMG -previous_db_calc_tax_stats_file -memory 3G
[command] -ss

