Metagenomic profiling and phylogenetic distances via common kmers
Python C++ Shell
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.

README.md

MetaPalette

What is MetaPalette?

MetaPalette is a k-mer based bacterial community reconstruction technique that utilizes sparsity promoting ideas from the field of compressed sensing to reconstruct the composition of a bacterial community. This method allows for strain-level abundance estimation, and can quantify the evolutionary distance between organisms in the sample and in the training database (thereby allowing for successful classification even with incomplete training data).

For the impatient

By far, the easiest way to run MetaPalette is to use Docker. The following demonstrates running MetaPalette on the included data:

#Get the Docker container
docker pull dkoslicki/metapalette

#Get the test data
cd ~
git clone https://github.com/dkoslicki/MetaPalette.git

#Train using MetaPalette
docker run --rm --privileged \
-e "DCKR_THREADS=10" \
-e "RAM_DISK_SIZE=10G" \
-v ~/MetaPalette/Tests/Data:/dckr/mnt/input:ro \ #Where the input training files live. Note the required file FileNames.txt listing the names of the training files.
-v ~/MetaPalette/Tests/TestOutput:/dckr/mnt/output:rw \ #Where you want the results to be saved
-t dkoslicki/metapalette train 

#Classify using MetaPalette
docker run --rm \
-e "QUALITY=C" \
-e "DCKR_THREADS=10" \
-e "TAXARANK=genus" \
-e "OUTGROUP=Escherichia_coli" \
-v ~/MetaPalette/Tests/TestOutput:/dckr/mnt/MetaPaletteData:ro \ #Location of the training data
-v ~/MetaPalette/Tests/TestOutput:/dckr/mnt/output:rw \ #Where you want the results to be saved
-v ~/MetaPalette/Tests/Data:/dckr/mnt/input:ro \ #Where the input sample files live. Note the required file InputFileNames.txt that gives a list of the sample files you wish to analyze.
-t dkoslicki/metapalette default 

The resulting profile, tree plots, and bar charts will be contained in ~/MetaPalette/Tests/TestOutput. Compare with the pre-computed results in ~/MetaPalette/Tests/Output.

To run MetaPalette using one of the pre-trained databases, use the following:

cd ~
wget http://files.cgrb.oregonstate.edu/Koslicki_Lab/MetaPalette/Bacteria.tar.gz #Or Archaea.tar.gz, Eukaryota.tar.gz, Viruses.tar.gz, Comparison.tar.gz (for the training database used in the paper for comparison purposes)
tar -xf Bacteria.tar.gz 
docker run --rm \
-e "QUALITY=C" \
-e "DCKR_THREADS=48" \
-e "TAXARANK=species" \
-e "OUTGROUP=Halobacterium_sp_DL1" \
-v ~/Bacteria:/dckr/mnt/MetaPaletteData:ro \ #Location of the training data
-v ~/path/to/output/folder:/dckr/mnt/output:rw \ #Where you want the results to be saved
-v ~/path/to/input/folder:/dckr/mnt/input:ro \ #Where the input sample files live. A file ~/path/to/input/folder/InputFileNames.txt MUST be present that gives a list of the sample files you wish to analyze
-t dkoslicki/metapalette default

How Do I Install MetaPalette?

Training Data

You can optionally download pre-trained data. Pre-trained data for Archaea, Bacteria, Eukaryota, and viruses are included.

Build from source

You will need the k-mer counting tool Jellyfish to be installed. Please see the Jellyfish installation page for installation directions. Briefly, this can be installed using:

mkdir /jellyfish
cd jellyfish
wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.3/jellyfish-2.2.3.tar.gz
tar -xf jellyfish-2.2.3.tar.gz
cd jellyfish-2.2.3
./configure
make

The binary will then be located in jellyfish-2.2.3/bin/.

You will need to compile the C code query_per_sequence contained in MetaPalette/src/QueryPerSeq/ (not the code in the Jellyfish examples). This can be accomplished with a command such as:

cd MetaPalette/src/QueryPerSeq
g++ -I /jellyfish/jellyfish-2.2.3/include -std=c++0x -Wall -O3 -L /jellyfish/jellyfish-2.2.3/.libs -Wl,--rpath=/jellyfish/jellyfish-2.2.3/.libs query_per_sequence.cc sequence_mers.hpp -l jellyfish-2.0 -l pthread -o query_per_sequence

The plotting features require ETE2 and a few other dependencies which can be installed with something like:

sudo apt-get install -y python-numpy python-qt4 python-lxml python-six python-matplotlib
easy_install -U ete2
apt-get install -y python-numpy python-scipy python-dev python-pip
apt-get install -y python-h5py

Or Use Docker

A Dockerfile is included in this repository. See the Docker homepage for more information.

You can either pull the docker image from DockerHub using

docker pull dkoslicki/metapalette

Or you can build the docker image from the Dockerfile by cloning the repository, starting Docker, and then in the MetaPalette/Docker folder, using the command:

docker build -t username/imagename .

Running the program

From the command line

To classify a sample, use the Classify.py command located in MetaPalette/src/Python. An example of running the program in the sensitive mode using 48 threads and a minimum quality score (for kmers to be counted) of C (phred33 ascii code 35) is given by

python Classify.py -d /path/to/MetaPaletteData/ -o /path/to/output_folder/ -i /path/to/input/file.fastq -Q C -k sensitive -j /path/to/./jellyfish -q /path/to/./query_per_sequence -t 48 -n 

FASTQ and FASTA files are acceptable input. Note that if FASTA files are used, no error correction will be done (which can lead to poor results).

The optional flag -n will normalize the output profile to sum to 1 (so it will appear that 100% of the sample has been classified). This is similar to the default options of MetAPhlAn.

Plotting Results

To generate tree figures, after running Classify.py, use the following commands:

python Plot.py -d /path/to/MetaPaletteData/ -o /path/to/outputFolder -p /path/to/ClassifyOutputFolder -i file.fastq -t <rank> -g <outgroup>

The flag -t specifies at what taxonomic rank the figures are to be made at. Acceptable values for <rank> include genus and species.

The flag -g specifies the outgroup for the tree figures. Default is Halobacterium_sp_DL1. This can be any organism name found in Taxonomy.txt.

To generate bar charts of the taxonomic profile, use:

python MakeBarChart.py -i /path/to/file.fastq.profile -o /path/to/outputFolder

Using Docker

To run the tool from docker, mount the appropriate folders and run using the following command:

docker run --rm -e "QUALITY=C" -e "DCKR_THREADS=48" -v /path/to/MetaPaletteData:/dckr/mnt/camiref/MetaPaletteData:ro -v /path/to/Output:/dckr/mnt/output:rw -v /path/to/Input:/dckr/mnt/input:ro -t username/imagename [type]

In the input folder must be a collection of gzipped FASTQ (or FASTA) files, as well as a file called sample.fq.gz.list (given by the docker image environmental variable $CONT_FASTQ_FILE_LISTING) listing the files on which to run the tool. Here [type] is one of default, sensitive, specific. The --rm flag deletes temporary files after exit (otherwise they might persist in /var/lib/docker/volumes or the like). If the environmental variable QUALITY is not passed to docker (via -e QUALITY=<ascii character>), a default value of "C" will be used.

Output format

The output format complies with the CAMI format. The docker complies with the Bioboxes profiling format 0.9.

Recommendations

I recommend using a quality score roughly equal to the average first quartile quality score in the file. This can be found with the following commands:

#Convert non ACTGN characters to N
awk '{if(NR%4==2){gsub(/[^ACGT]/,"N");print $0}else{print $0}}' input.fq > input_ACTGN.fq 
#Compute average first quartile quality score
/Fastx/bin/./fastx_quality_stats -i input_ACTGN.fq -Q33 | cut -f7 | sed -n '1!p' | awk '{a+=$1} END{print a/NR}' | awk '{printf "%.0f",$1}'

The FastX toolbox can be downloaded here.

Custom Training Databases

If you wish to use a custom training database, the following steps must be performed:

  1. Install Bcalm
  2. Create a directory to contain the training data (called MetaPaletteTrainingData below).
  3. Create an acceptable taxonomy for the training genomes, and place it in the MetaPaletteTrainingData folder.
  4. Create a file consisting of the full paths of the training genomes, and save this to a file FileNames.txt.
  5. Compile the code contained in MetaPalette/src/CountInFile/.
  6. Run the script Train.py.

Alternatively, you can use Docker (though an acceptable taxonomy still needs to be created).

Install Bcalm

To install Bcalm, do something like the following:

wget https://github.com/Malfoy/bcalm/archive/1.tar.gz && \
 tar -zxf 1.tar.gz && \
 cd bcalm-1 && \
 make && \
 cp bcalm /usr/local/bin

Note that the current Bcalm git repository does not compile correctly, so you must install from the release.

Creating custom taxonomy

For each genome in FileNames.txt (and in the same order), a taxonomy file must be created. This file MUST be a newline delimitated file with each line having the following format:

<organismName>\t<TaxID>\t<TaxPath>

<organismName> must be a unique identifier for each genome.

<TaxID> must be a unique TaxID for each genome

<TaxPath> must be a pipe delimitated list that gives the taxonomy of the given organism. The format is:

k__<KingdomTaxID>_<KingdomName>|p__<PhylumTaxID>_<PhylumName>|c__<ClassTaxID>_<ClassName>|o__<OrderTaxID>_<OrderName>|f__<FamilyTaxID>_<FamilyName>|g__<GenusTaxID>_<GenusName>|s__<SpeciesTaxID>_<SpeciesName>|t__<StrainTaxID>_<StrainName>

The taxonomy is only required at the kingdom level, with lower levels being optional. Missing ranks can be included with ||.

An example line is as follows:

1184607_Austwickia_chelonae_NBRC_105200	1184607	k__2_Bacteria|p__201174_Actinobacteria|c__1760_Actinobacteria|o__2037_Actinomycetales|f__85018_Dermatophilaceae|g__1184606_Austwickia|s__100225_Austwickia_chelonae|t__1184607_Austwickia_chelonae_NBRC_105200

For your convenience, scripts are included in MetaPalette/src/NCBIDatabase to assist in using the NCBI taxonomy and organisms obtained via RepoPhlAn. These can be run via:

./run.sh

This will automatically download all Archaea, Bacteria, Eukaryota, and viruses, and create the corresponding Taxonomy.txt files.

Compile the count_in_file code

The /MetaPalette/src/CountInFile/count_in_file.cc code can be compiled using a command like:

cd MetaPalette/src/CountInFile
g++ -I /jellyfish/jellyfish-2.2.3/include -std=c++0x -Wall -O3 -L /jellyfish/jellyfish-2.2.3/.libs -Wl,--rpath=/jellyfish/jellyfish-2.2.3/.libs count_in_file.cc -l jellyfish-2.0 -l pthread -o count_in_file

Run the script Train.py

The script Train.py can be called using a command such as:

python Train.py -i FileNames.txt -o /path/to/output/MetaPaletteTrainingData/ -b /path/to/./bcalm -r /path/to/fast/IO/device/ -j /path/to/jellyfish -c /path/to./count_in_file -s 500 -t 48 -k 20

The option -s specifies how many training genomes at a time are held in memory. Increasing/decreasing this increases/decreases the amount of RAM used.

The option -k specifies how many jellyfish instances are created. Too many will cause disk thrashing (default is 20).

The option -r specifics the location of a temporary folder on a fast IO device. Unfortunately Bcalm uses a considerable amount of file IO, and so a fast storage device is required. Note that you can create a RAM disk using a command like:

mkdir /tmp/ramdisk; chmod 777 /tmp/ramdisk
sudo mount -t tmpfs -o size=100G tmpfs /tmp/ramdisk/

To unmount the RAM disk, use a command like:

sudo umount -v /tmp/ramdisk

Note that the time required to complete the training step can be considerable (depending on hardware available). Using 48 cores and 256GB of RAM, training on ~7,000 genomes can take a number of days.

Using Docker

Alternatively, after creating the acceptable taxonomy, Docker can be used to form the training data. You will need to have access to a folder containing all the uncompressed training fasta/fastq files. You will also need to create a file (name it sample.fna.list) that contains all the base names of the training fasta/fastq files, and put this in the same folder.

Docker can then be called with

docker run --rm --privileged -e "DCKR_THREADS=48"  -e "RAM_DISK_SIZE=100G" -v /path/to/input/data:/dckr/mnt/input:ro -v /path/to/output/folder:/dckr/mnt/output:rw -t username/imagename train

The flag --privileged is required since docker will then be allowed to automatically create the RAM disk. Note the default RAM disk size is 10G (I suggest using around half the available RAM).

Run the Classify.py script

You can now run the Classify.py script as before, but this time utilizing the directory MetaPaletteTrainingData for the option -d.

Contact

For issues with this software, contact david.koslicki@math.oregonstate.edu. Otherwise, submit an issue directly through Github.

License

This project is released under the GPL-3 License. Please view the LICENSE file for more details.

Contributors

  • David Koslicki (all main source code, unless otherwise noted)
  • Daniel Alonso Alemany (early version of the software)
  • Daniel Falush
  • Nam Nguyen