Kraken2 is a taxonomic sequence classification system. This project builds on the classification functionality to provide a server-client architecture to allow two use cases:
- Access to the classification algorithms in low-resource settings by sending requests to remote, more powerful servers
- One-time loading of databases (a slow step compared to classification) into a persistent process, with subsequent independent classification requests as data becomes available
The software is currently a public beta release.
The kraken2 server and client are available through our conda channel:
mamba create -n kraken2 -c conda-forge -c nanoporetech kraken2-server
To start a server run:
kraken2_server --db <db_path>
where <db_path> is a directory containing a standard kraken2 database. The
server will wait for requests for clients and respond as necessary.
To classify reads run a client with:
kraken2_client --port 8080 --sequence <reads.fq.gz>
where <reads.fq.gz> can be FASTQ or FASTA either plain text or gzip compressed.
The output gives some of the same details as running the standard
kraken2 program. Currently it is not identical; the intention is to
in future provide compatible output.
The project can be built with cmake >3.13 and a C++17 compiler.
The server-client architecture uses gRPC and protobuf to communicate. An installation of gRPC (with protobuf is required).
The following should be sufficient to setup an installation of gRPC and protobuf (see gRPC Dependencies for C++):
INSTALL_ROOT=$PWD # or something else
# this flag might be needed on some platforms
export LDFLAGS="-lrt"
export PROTO_DIR=$INSTALL_ROOT/proto-build
export PATH="$PROTO_DIR/bin:$PATH"
mkdir -p $PROTO_DIR
git clone --recurse-submodules -b v1.46.3 --depth 1 --shallow-submodules https://github.com/grpc/grpc
mkdir -p grpc/cmake/build
pushd grpc/cmake/build
cmake -DgRPC_INSTALL=ON \
-DgRPC_BUILD_TESTS=OFF \
-DCMAKE_INSTALL_PREFIX=$PROTO_DIR \
../..
make -j
make install
popd
To build the project itself then run:
git clone https://github.com/epi2me-labs/kraken2-server.git`
cd kraken2-server
mkdir build
pushd build
# PROTO_DIR as above
cmake -DCMAKE_PREFIX_PATH=${PROTO_DIR} --config Release ..
make -j 8
popd
The server and client executables will be written to:
build/server/kraken2_server
build/client/kraken2_client
Benchmarking script from testing/run_server.sh
Single client test
MacBook Pro 14-inch 2021, M1 Max, 64Gb. macOS 13.2.1. Clang 13.1.6. 1190.33 Mbp per client
| clients | server threads | client time / s | server throughput / Mbp/m |
|---|---|---|---|
| 1 | 2 | 48.8 | 1462 |
| 1 | 4 | 25.1 | 2839 |
| 1 | 6 | 18.4 | 3876 |
| 1 | 8 | 16.8 | 4237 |
Multi client test
Intel Xeon Gold 6230, Ubuntu 16.04.7, gcc 11.3.0. 991.94 Mbp per client
| clients | server threads | client time / s | server throughput / Mbp/m |
|---|---|---|---|
| 1 | 64 | 19.8 | 3011 |
| 2 | 64 | 21.6 | 5491 |
| 4 | 64 | 24.1 | 9802 |
| 8 | 64 | 28.9 | 16335 |
| 16 | 64 | 62.2 | 14958 |