mkdir MY_CHECKM_FOLDER

# Now manually download the database:
cd MY_CHECKM_FOLDER
wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
tar -xvf *.tar.gz
rm *.gz
cd ../

# Now you need to tell CheckM where to find this data before running anything:
checkm data setRoot     # CheckM will prompt to to chose your storage location
# On newer versions of CheckM, you would run:
checkm data setRoot /path/to/your/dir/MY_CHECKM_FOLDER

Thats it! CheckM should now use that folder and its contents as its database.

Note: As of metaWRAP v1.3.2, we recomend you use Kraken2 instead of the original Kraken1 (see below). Note: this will download the entire RefSeq database and index it, which takes a lot of computational power, storage space, and RAM. During database building, you will need >450GB of space and >250GB of RAM. With 24 cores, this will take >5 hours. Note that this is only needed if you intend on running the KRAKEN module.

kraken-build --standard --threads 24 --db MY_KRAKEN_DATABASE
kraken-build --db MY_KRAKEN_DATABASE --clean

Do not forget to set the KRAKEN_DB variable in the config-metawrap file! Run which config-metawrap to find it.

KRAKEN_DB=/path/to/my/database/MY_KRAKEN_DATABASE

Note: Compared to Kraken1, the Kraken2 database is considerably more compact, making the download and indexing process much faster and less taxing on the system. You will need an estimated 120GB of RAM and ~128GB of space. Note that this is only needed if you intend on running the KRAKEN2 module.

kraken2-build --standard --threads 24 --db MY_KRAKEN2_DB

Do not forget to set the KRAKEN_DB variable in the config-metawrap file! Run which config-metawrap to find it.

KRAKEN2_DB=/path/to/my/database/MY_KRAKEN2_DATABASE

mkdir NCBI_nt
cd  NCBI_nt
wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.tar.gz"
for a in nt.*.tar.gz; do tar xzf $a; done

Note: if you are using a more recent blast verions (beyond v2.6) you will need a the newer database format: wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/v4/nt_v4.*.tar.gz"

Do not forget to set the BLASTDB variable in the config-metawrap file!

BLASTDB=/your/location/of/database/NCBI_nt

mkdir NCBI_tax
cd NCBI_tax
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
tar -xvf taxdump.tar.gz

Do not forget to set the TAXDUMP variable in the config-metawrap file! Run which config-metawrap to find it.

TAXDUMP=/your/location/of/database/NCBI_tax

If you want to remove human (see end of instrutions for non-human hosts) reads from tour sequencing in the READ_QC module, you will need to dowlnoad and index the human genome. See the official bmtagger manual for detailed instructions: https://www.hmpdacc.org/hmp/doc/HumanSequenceRemoval_SOP.pdf

First, lets download and merge the human genome hg38:

mkdir BMTAGGER_INDEX
cd BMTAGGER_INDEX
wget ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/*fa.gz
gunzip *fa.gz
cat *fa > hg38.fa
rm chr*.fa

Now lets index the human genome. Note that the file names of the indeces must be exactly as specified for metaWRAP to recognize them! Also note that indexing will take considerable memory and time (here I pass 100GB of RAM as a -M parameter).

bmtool -d hg38.fa -o hg38.bitmask
srprism mkindex -i hg38.fa -o hg38.srprism -M 100000

Note: metaWRAP looks for files hg38.bitmask and hg38.srprism - make sure they are names exactly like this. Done! Now dont forget to specify the BMTAGGER_DB variable in the config-metawrap file! Run which config-metawrap to find it.

BMTAGGER_DB=/path/to/your/index/BMTAGGER_INDEX

For non-human hosts, the protocol for building and using the bmtagger index should be the same. In the end, you need to have th .srprism and .bitmask index files in the BMTAGGER_INDEX directory that you will link to in the config-metawrap file. When you run metawrap read_qc, you need to use the -x option to specify the prefix of your host. For example, if your BMTAGGER_INDEX directory has files pig.srprism and pig.bitmask, use -x pig as the option.