HPV-Kite is a Java application that detects HPV within samples. It can be used for DNA and/or RNA FASTQ files.
KITE stands for K-mer Index Tversky Estimator, as the application leverages k-mer analysis combined with the Tversky index.
HPV-Kite not only expedites viral detection but also maintains comparable sensitivity to existing approaches.
The sample database of 222 HPV viruses generated 2024-02-23 from The PapillomaVirus Episteme (PaVE) database is embedded into the output JAR file. Still, it can also be any FASTA file with nucleotide sequences proceeded by descriptions of them.
To run the application Java Runtime Environment, at least in version 17, is required.
You can check the available version of the Java on the system by invoking the command: java -version in the terminal
window.
It would produce output like:
openjdk version "22.0.1" 2024-04-16 OpenJDK Runtime Environment (build 22.0.1+8-16) OpenJDK 64-Bit Server VM (build 22.0.1+8-16, mixed mode, sharing)
That means that Java in version 22 is installed on the computer, so it meets the requirement.
If the java command is not found, that can mean that the command is not in the PATH or Java is not installed at all.
You can easily install the current ready-to-use version from https://jdk.java.net/ just by downloading the version that
is adequate for your operating system.
The application uses the PCJ library (GitHub repository) to process files concurrently using the multinode environment. It uses PCJ in version 5.3.3. The jar file with the PCJ library is attached in a release zip file.
Building the application from source code
The Gradle build system is used to manage dependencies and build software. It is possible to build the application from
the source code, by calling:
./gradlew assemble or gradlew.bat assemble.
Other useful Gradle tasks: createDependenciesJar, createFatJar.
The current version of the application is available on the Release page. The release is packed as a ZIP file that has to be unpacked into a local directory.
To run the application, just run the following command:
java -jar hpv-kite-1.0.jar <list-of-file-paths.fq.gz>
For example:
java -jar hpv-kite-1.0.jar *.fq.gz
Click to see command output
It would produce output like:maj 22, 2024 12:33:40 PM org.pcj.internal.InternalPCJ start INFO: PCJ version 5.3.3-831a4fa (2023-10-10T14:35:07.064+0200) maj 22, 2024 12:33:41 PM org.pcj.internal.InternalPCJ start INFO: Starting pl.edu.icm.heap.kite.PcjMain with 1 thread (on 1 node)... [2024-05-22 12:33:41,806] shingleLength = 31 [2024-05-22 12:33:41,807] gzipBuffer = 512 [2024-05-22 12:33:41,807] readerBuffer = 512 [2024-05-22 12:33:41,808] processingBuffer = 64 [2024-05-22 12:33:41,809] threadPoolSize = 8 [2024-05-22 12:33:41,809] outputHpvCount = 3 [2024-05-22 12:33:41,810] hpvVirusesPath = <bundled> [2024-05-22 12:33:41,813] Files to process (3): [sample_00005.fq.gz, sample_00064.fq.gz, sample_08414_without.fq.gz] [2024-05-22 12:33:41,813] filesGroupPattern = <none> [2024-05-22 12:33:41,814] Reading HPV viruses file by all threads... takes 0,894718 [2024-05-22 12:33:42,697] Loaded 222 HPV viruses: [HPV69REF, HPV82REF, HPV71REF, HPV126REF, HPV160REF, HPV85REF, HPV83REF, HPV84REF, HPV86REF, HPV91REF, HPV89REF, HPV74REF, HPV92REF, HPV87REF, HPV43REF, HPV81REF, HPV95REF, HPV94REF, HPV90REF, HPV93REF, HPV96REF, HPV62REF, HPV67REF, HPV58REF, HPV103REF, HPV68REF, HPV97REF, HPV101REF, HPV106REF, HPV102REF, HPV107REF, HPV88REF, HPV110REF, HPV111REF, HPV109REF, HPV112REF, HPV116REF, HPV115REF, HPV108REF, HPV98REF, HPV99REF, HPV100REF, HPV104REF, HPV105REF, HPV113REF, HPV125REF, HPV150REF, HPV151REF, HPV114REF, HPV117REF, HPV118REF, HPV119REF, HPV120REF, HPV121REF, HPV122REF, HPV123REF, HPV124REF, HPV149REF, HPV130REF, HPV131REF, HPV132REF, HPV133REF, HPV134REF, HPV148REF, HPV128REF, HPV129REF, HPV159REF, HPV174REF, HPV179REF, HPV184REF, HPV127REF, HPV135REF, HPV136REF, HPV137REF, HPV138REF, HPV139REF, HPV140REF, HPV141REF, HPV142REF, HPV143REF, HPV144REF, HPV145REF, HPV146REF, HPV147REF, HPV31REF, HPV152REF, HPV155REF, HPV153REF, HPV154REF, HPV166REF, HPV169REF, HPV164REF, HPV163REF, HPV162REF, HPV161REF, HPV170REF, HPV156REF, HPV165REF, HPV16REF, HPV175REF, HPV180REF, HPV78REF, HPV168REF, HPV167REF, HPV171REF, HPV172REF, HPV173REF, HPV178REF, HPV199REF, HPV197REF, HPV200REF, HPV201REF, HPV202REF, HPV204REF, HPV176REF, HPV177REF, HPV181REF, HPV182REF, HPV183REF, HPV185REF, HPV186REF, HPV187REF, HPV188REF, HPV189REF, HPV190REF, HPV191REF, HPV192REF, HPV193REF, HPV194REF, HPV195REF, HPV196REF, HPV157REF, HPV205REF, HPV158REF, HPV209REF, HPV33REF, HPV8REF, HPV11REF, HPV5REF, HPV47REF, HPV39REF, HPV51REF, HPV42REF, HPV224REF, HPV211REF, HPV212REF, HPV213REF, HPV214REF, HPV215REF, HPV216REF, HPV223REF, HPV225REF, HPV226REF, HPV203REF, HPV219REF, HPV220REF, HPV221REF, HPV222REF, HPV210REF, HPV227REF, HPV207REF, HPV208REF, HPV229REF, HPV228REF, HPV70REF, HPV20REF, HPV21REF, HPV22REF, HPV23REF, HPV24REF, HPV28REF, HPV29REF, HPV36REF, HPV37REF, HPV38REF, HPV44REF, HPV48REF, HPV50REF, HPV60REF, HPV61REF, HPV66REF, HPV54REF, HPV206REF, HPV1REF, HPV6REF, HPV18REF, HPV2REF, HPV57REF, HPV41REF, HPV13REF, HPV4REF, HPV63REF, HPV65REF, HPV3REF, HPV7REF, HPV9REF, HPV10REF, HPV12REF, HPV14REF, HPV15REF, HPV17REF, HPV19REF, HPV25REF, HPV26REF, HPV27REF, HPV30REF, HPV32REF, HPV34REF, HPV35REF, HPV40REF, HPV45REF, HPV49REF, HPV52REF, HPV53REF, HPV56REF, HPV59REF, HPV72REF, HPV73REF, HPV75REF, HPV76REF, HPV77REF, HPV80REF] <... processing ...> [2024-05-22 12:33:44,699] Total time: 2,897480500 maj 22, 2024 12:33:44 PM org.pcj.internal.InternalPCJ start INFO: Completed pl.edu.icm.heap.kite.PcjMain with 1 thread (on 1 node) after 0h 0m 2s 959ms.
HPV-KITE has multiple parameters that can be used for the run.
The following tables show the names of the parameters with their default values and meaning.
| parameter name | default value | description |
|---|---|---|
| shingleLength | 31 | list of comma separated values for K-mer length (e.g. 18 or 30,32) |
| outputHpvCount | 3 | maximum number of HPV viruses that match index is returned; if non-positive - return results for all HPV viruses from the database |
| hpvVirusesPath | bundled | path to the FASTA files with HPV viruses database; if not provided, the application will use embedded database |
| filesGroupPattern | "" (empty string) | regular expression pattern to group results from multiple input files; empty string means not to group results |
| nodesFile | nodes.txt | file with names of the nodes which will be used to start multinode processing |
| deploy | false | flag to tell that application should use deploy mechanism of the PCJ library (SSH connection) to start computation in multinode processing; if set to false, it is necessary to start processing files in multinode environment using available mechanisms like srun, aprun, mpiexec. |
| threadPoolSize | available CPUs | number of threads that is processing data |
| processingBuffer | 64 | minimal size of buffer for characters to start processing data concurrently (in KB) |
| gzipBuffer | 512 | internal buffer size for loading GZIP files (in KB) |
| readerBuffer | 512 | internal buffer size for reading FASTQ files (in KB) |
To modify the parameter, just give its name with the -D prefix (e.g. -DshingleLength=30) at the beginning of the
command line just after java.
For example:
java \
-DshingleLength=30 \
-DoutputHpvCount=1 \
-jar hpv-kite-1.0.jar \
sample_00005.fq.gz sample_00064.fq.gz sample_08414_without.fq.gzIt will start processing 3 files (sample_00005.fq.gz, sample_00064.fq.gz, and sample_08414_without.fq.gz) on the
local machine, returning the index only for the most similar HPV virus (-DoutputHpvCount=1) using the 30-character
long shingles (k-mers; -DshingleLength=30).
java \
-DshingleLength=30 \
-DnodesFile=all_nodes.txt \
-Ddeploy=true \
-DoutputHpvCount=1 \
-DfilesGroupPattern='sample_0[0-9]' \
-jar hpv-kite-1.0.jar \
sample_00005.fq.gz sample_00064.fq.gz sample_08414_without.fq.gzThe command will start processing 3 files (sample_00005.fq.gz, sample_00064.fq.gz, and sample_08414_without.fq.gz)
like in the example above, but on nodes described in all_nodes.txt file (-DnodesFile=all_nodes.txt).
all_nodes.txt file
The all_nodes.txt file should have the hostname of each node in a separate line, e.g.:
wn8001
wn8002
wn8003
It will start computation on these nodes using SSH connection (-Ddeploy=true).
Note
Be sure that HPV-Kite jar files (hpv-kite-1.0.jar and pcj-5.3.3.jar) are located in the same path as in the
calling machine.
This is normal in most of the computer clusters.
However, then you are probably using mpiexec, srun or another command to run parallel jobs, so you do not have
to use deploy mechanism.
Shingles from multiple input files will be grouped (-DfilesGroupPattern='sample_0[0-9]') to generate summary result
for these groups:
- sample_00 (files:
sample_00005.fq.gzandsample_00064.fq.gz), - sample_08 (file:
sample_08414_without.fq.gz).
Click to see command output
The command would produce the following information in a header:maj 22, 2024 1:23:56 PM org.pcj.internal.InternalPCJ start INFO: PCJ version 5.3.3-831a4fa (2023-10-10T14:35:07.064+0200) maj 22, 2024 1:23:57 PM org.pcj.internal.InternalPCJ start INFO: Starting pl.edu.icm.heap.kite.PcjMain with 1 thread (on 1 node)... [2024-05-22 13:23:57,657] shingleLength = 30 [2024-05-22 13:23:57,657] gzipBuffer = 512 [2024-05-22 13:23:57,657] readerBuffer = 512 [2024-05-22 13:23:57,658] processingBuffer = 64 [2024-05-22 13:23:57,658] threadPoolSize = 8 [2024-05-22 13:23:57,659] outputHpvCount = 1 [2024-05-22 13:23:57,659] hpvVirusesPath = <bundled> [2024-05-22 13:23:57,661] Files to process (3): [sample_00005.fq.gz, sample_00064.fq.gz, sample_08414_without.fq.gz] [2024-05-22 13:23:57,662] filesGroupPattern = sample_0[0-9] [2024-05-22 13:23:57,668] File groups (2): [sample_00, sample_08] <... further processing ...>
When using the tool in published research, please cite:
under review, please come back soon