jvarkit

VcfJmx

Monitor/interrupt/break a VCF stream with java JMX http://www.oracle.com/technetwork/articles/java/javamanagement-140525.html

Usage

Usage: vcfjmx [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output vcf , ot stdin
    --version
      print version and exit
    -p
      Stream identifier

Keywords

• java
• jmx
• vcf

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfjmx

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/jmx/VcfJmx.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite vcfjmx ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Example

$   java -jar dist/vcfjmx.jar -p MyWorkflow1 input.vcf > /dev/null

while the stream is running, open a new jconsole https://docs.oracle.com/javase/7/docs/technotes/guides/management/jconsole.html . here you can get the number of records, the elapsed time. Two operation are available:

• doBreak: interrupt current streaming , exit with success (0)
• doAbort: interrupt current streaming , exit with failure (-1)

$ java -jar dist/vcfjmx.jar -p 1000G  ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.vcf.gz | \
    java -jar dist/vcfjmx.jar  -p 1000G-2  |\
    java -jar dist/vcfjmx.jar  -p 1000G-3  |\
    java -jar dist/vcfjmx.jar  -p 1000G-4 > /dev/null

[INFO/VcfJmx] 2015-07-10 14:11:08 "Starting JOB at Fri Jul 10 14:11:08 CEST 2015 com.github.lindenb.jvarkit.tools.jmx.VcfJmx version=4f797a9fbf2c3ceac9cec3c431c719ad794953c2  built=2015-07-10:13-07-05"
[INFO/VcfJmx] [INFO/VcfJmx] 2015-07-10 14:11:08 "Command Line args : -p 1000G-2"
2015-07-10 14:11:08 "Starting JOB at Fri Jul 10 14:11:08 CEST 2015 com.github.lindenb.jvarkit.tools.jmx.VcfJmx version=4f797a9fbf2c3ceac9cec3c431c719ad794953c2  built=2015-07-10:13-07-05"
[INFO/VcfJmx] 2015-07-10 14:11:08 "Command Line args : -p 1000G-3"
[INFO/VcfJmx] 2015-07-10 14:11:08 "Starting JOB at Fri Jul 10 14:11:08 CEST 2015 com.github.lindenb.jvarkit.tools.jmx.VcfJmx version=4f797a9fbf2c3ceac9cec3c431c719ad794953c2  built=2015-07-10:13-07-05"
[INFO/VcfJmx] 2015-07-10 14:11:08 "Command Line args : -p 1000G ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.vcf.gz"
[INFO/VcfJmx] 2015-07-10 14:11:08 "Executing as lindenb@kaamelot-master01 on Linux 2.6.32-431.17.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_60-b19"
[INFO/VcfJmx] 2015-07-10 14:11:08 "Executing as lindenb@kaamelot-master01 on Linux 2.6.32-431.17.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_60-b19"
[INFO/VcfJmx] 2015-07-10 14:11:08 "Executing as lindenb@kaamelot-master01 on Linux 2.6.32-431.17.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_60-b19"
[INFO/VcfJmx] 2015-07-10 14:11:08 "reading from stdin"
[INFO/VcfJmx] 2015-07-10 14:11:08 "reading from stdin"
[INFO/VcfJmx] 2015-07-10 14:11:08 "reading from ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.vcf.gz"

[SEVERE/VcfJmx] 2015-07-10 14:11:46 "#### Process "1000G-3" received message BREAK"

[INFO/VcfJmx] 2015-07-10 14:11:46 "Number of Variants:1130774"
[INFO/VcfJmx] 2015-07-10 14:11:46 "End JOB status=0 [Fri Jul 10 14:11:46 CEST 2015] com.github.lindenb.jvarkit.tools.jmx.VcfJmx done. Elapsed time: 0.64 minutes."
[INFO/VcfJmx] 2015-07-10 14:11:46 "Number of Variants:1120774"
[INFO/VcfJmx] 2015-07-10 14:11:46 "Number of Variants:1110975"
[INFO/VcfJmx] 2015-07-10 14:11:46 "End JOB status=0 [Fri Jul 10 14:11:46 CEST 2015] com.github.lindenb.jvarkit.tools.jmx.VcfJmx done. Elapsed time: 0.64 minutes."
[INFO/VcfJmx] 2015-07-10 14:11:46 "End JOB status=0 [Fri Jul 10 14:11:46 CEST 2015] com.github.lindenb.jvarkit.tools.jmx.VcfJmx done. Elapsed time: 0.64 minutes."

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