安装 VarDictJava

【VarDictJava】

2019/6/5 17:21:14
安装VarDictJava的时候，始终报错，
最后跟原作者的沟通中发现：
Well, I see in the path, that this folder is mounted (i.e. it is shared file system). Can you build VarDictJava in your local folder? I know that there are some problems in Gradle with mounted folders on some types of file systems.
After you build it, you can copy folder build\install\VarDict that will be created, for further using, it contains all libraries and scripts that you need.

也就是说： /mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software 是“shared file system”， 它是“mounted ”
而在mounted folders on some“shared file system”， Gradle 可能出错。

后来我这样做了，然后另一个问题出现了：

===========================================
[fengyuzhe@login2 ~/01.Program/02.software/VarDictJava]

$./gradlew clean installDist

> Task :compileJava FAILED

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':compileJava'.
> Could not target platform: 'Java SE 8' using tool chain: 'JDK 7 (1.7)'.

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Get more help at https://help.gradle.org

Deprecated Gradle features were used in this build, making it incompatible with Gradle 5.0.
Use '--warning-mode all' to show the individual deprecation warnings.
See https://docs.gradle.org/4.10.2/userguide/command_line_interface.html#sec:command_line_warnings

BUILD FAILED in 25s
2 actionable tasks: 1 executed, 1 up-to-date
===========================================

原作者说：
That means that your local version of Java is Java 7. We support only Java 8 and higher.
我回答：
I don't think so:

=================================================================
$which java
~/01.Program/02.software/miniconda3/bin/java

[fengyuzhe@login2 /mnt/lustre/user/fengyuzhe/03.Clinical_Data/01.Germline/sh.e.o/B190010_caitian-1_DX0512]
$java -version
openjdk version "1.8.0_152-release"
OpenJDK Runtime Environment (build 1.8.0_152-release-1056-b12)
OpenJDK 64-Bit Server VM (build 25.152-b12, mixed mode)
=================================================================

原作者：
Your echo $JAVA_HOME is set to /usr/java/latest, and this version will be used by Gradle. I guess this folder contains JDK 1.7. You can set JAVA_HOME to the path where you have Java 8.

我：

Thanks for your patience, do you mean this?
==========================================
echo 'export JAVA_HOME="/home/fengyuzhe/01.Program/02.software/miniconda3/bin"' >>~/.bashrc
==========================================
原作者：
Yes, please try to change it and rerun build. I hope it will help!
我：
thanks a lot for your patience, but,  it didn't help when I

echo 'export JAVA_HOME="/home/fengyuzhe/01.Program/02.software/miniconda3/bin"' >>~/.bashrc

[fengyuzhe@login2 ~/01.Program/02.software/VarDictJava]
$bash
[fengyuzhe@login2 ~/01.Program/02.software/VarDictJava]
$./gradlew clean installDist
Error: could not find libjava.so
Error: Could not find Java SE Runtime Environment.

原作者：
Did you reload bash after adding JAVA_HOME to bashrc? With source ~/.bashrc, for example?
我：
yes, you can see that I

[fengyuzhe@login2 ~/01.Program/02.software/VarDictJava]
$bash
[fengyuzhe@login2 ~/01.Program/02.software/VarDictJava]
$./gradlew clean installDist
Error: could not find libjava.so
Error: Could not find Java SE Runtime Environment.
原作者：
Can you show what are environmental variables for java now?
env | grep -i java
And also I check my configurations where miniconda is installed, JAVA_HOME is /home/user/miniconda3 , i.e. without bin folder in path. Could you try this?

我：
$env | grep -i java
MANPATH=/opt/gridengine/man:/opt/gridengine/man:/opt/gridengine/man:/mnt/lustre/user/fengyuzhe/01.Program/02.software/perlbrew/perls/perl-5.10.1/man:/opt/gridengine/man:/usr/share/man/en:/usr/share/man:/usr/local/share/man:/usr/java/latest/man:/opt/rocks/man:/opt/ganglia/man:/opt/openmpi/share/man:/opt/sun-ct/man
PATH=/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/Seq2C/plotting:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/Seq2C:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/VarDict:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/quast-5.0.2:/opt/rocks/mysql/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/bowtie/bowtie-0.12.7:/home/fengyuzhe/.aspera/connect/bin:/home/fengyuzhe/01.Program/02.software/miniconda3/bin:/home/fengyuzhe/01.Program/02.software/mothur/blast/bin:/home/fengyuzhe/01.Program/02.software/mothur:/home/fengyuzhe/01.Program/02.software/Binning:/mnt/lustre/user/fengyuzhe/01.Program/02.software/perlbrew/perls/perl-5.10.1/bin:/mnt/lustre/user/fengyuzhe/01.Program/02.software/perlbrew/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/sratoolkit.2.8.2-1-centos_linux64/bin:/mnt/lustre/user/fengyuzhe/01.Program/02.software/miniconda2/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/mothur/mothur/blast/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/mothur/mothur:~/.local/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/RepeatMasker:/drigen/BioSoftA/vcftools/vcftools_0.1.10/install/bin:/drigen/BioSoftB/exome_pipeline/shenyulanTest/software/tabix-0.2.6:/drigen/BioSoftB/exome_pipeline/annovar:/drigen/BioSoftA/perl/5.16.3/install/bin:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/sun-ct/bin:/opt/blc/genome/bin:/share/raid1/genome/bin:/share/raid1/genome/bin:/opt/blc/genome/bin:/opt/blc/genome/bin:opt/blc/self-software/bin:/opt/gridengine/lib/lx26-amd64:/opt/gridengine/lib/lx26-amd64:/usr/lib/oracle/11.1.0.1/client64/lib:/drigen/BioSoftA/R/2.15.3/install/bin:/drigen/BioSoftB/exome_pipeline/software/soap2.21release:/opt/gridengine/bin:/opt/gridengine/bin/lx-amd64:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/Seq2C/plotting:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/Seq2C:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/VarDict:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/quast-5.0.2:/opt/rocks/mysql/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/bowtie/bowtie-0.12.7:/home/fengyuzhe/.aspera/connect/bin:/home/fengyuzhe/01.Program/02.software/miniconda3/bin:/home/fengyuzhe/01.Program/02.software/mothur/blast/bin:/home/fengyuzhe/01.Program/02.software/mothur:/home/fengyuzhe/01.Program/02.software/Binning:/mnt/lustre/user/fengyuzhe/01.Program/02.software/perlbrew/perls/perl-5.10.1/bin:/mnt/lustre/user/fengyuzhe/01.Program/02.software/perlbrew/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/sratoolkit.2.8.2-1-centos_linux64/bin:/mnt/lustre/user/fengyuzhe/01.Program/02.software/miniconda2/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/mothur/mothur/blast/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/mothur/mothur:~/.local/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/RepeatMasker:/drigen/BioSoftA/vcftools/vcftools_0.1.10/install/bin:/drigen/BioSoftB/exome_pipeline/shenyulanTest/software/tabix-0.2.6:/drigen/BioSoftB/exome_pipeline/annovar:/drigen/BioSoftA/perl/5.16.3/install/bin:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/sun-ct/bin:/opt/blc/genome/bin:/share/raid1/genome/bin:/share/raid1/genome/bin:/opt/blc/genome/bin:/opt/blc/genome/bin:opt/blc/self-software/bin:/opt/gridengine/lib/lx26-amd64:/opt/gridengine/lib/lx26-amd64:/usr/lib/oracle/11.1.0.1/client64/lib:/drigen/BioSoftA/R/2.15.3/install/bin:/drigen/BioSoftB/exome_pipeline/software/soap2.21release:/opt/gridengine/bin:/opt/gridengine/bin/lx-amd64:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/Seq2C/plotting:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/Seq2C:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/VarDict:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/quast-5.0.2:/opt/rocks/mysql/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/bowtie/bowtie-0.12.7:/home/fengyuzhe/.aspera/connect/bin:/home/fengyuzhe/01.Program/02.software/miniconda3/bin:/home/fengyuzhe/01.Program/02.software/mothur/blast/bin:/home/fengyuzhe/01.Program/02.software/mothur:/home/fengyuzhe/01.Program/02.software/Binning:/mnt/lustre/user/fengyuzhe/01.Program/02.software/perlbrew/perls/perl-5.10.1/bin:/mnt/lustre/user/fengyuzhe/01.Program/02.software/perlbrew/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/sratoolkit.2.8.2-1-centos_linux64/bin:/mnt/lustre/user/fengyuzhe/01.Program/02.software/miniconda2/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/mothur/mothur/blast/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/mothur/mothur:~/.local/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/RepeatMasker:/drigen/BioSoftA/vcftools/vcftools_0.1.10/install/bin:/drigen/BioSoftB/exome_pipeline/shenyulanTest/software/tabix-0.2.6:/drigen/BioSoftB/exome_pipeline/annovar:/drigen/BioSoftA/perl/5.16.3/install/bin:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/sun-ct/bin:/opt/blc/genome/bin:/share/raid1/genome/bin:/share/raid1/genome/bin:/opt/blc/genome/bin:/opt/blc/genome/bin:opt/blc/self-software/bin:/opt/gridengine/lib/lx26-amd64:/opt/gridengine/lib/lx26-amd64:/usr/lib/oracle/11.1.0.1/client64/lib:/drigen/BioSoftA/R/2.15.3/install/bin:/drigen/BioSoftB/exome_pipeline/software/soap2.21release:/opt/gridengine/bin:/opt/gridengine/bin/lx-amd64:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/Seq2C/plotting:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/Seq2C:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/VarDict:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/quast-5.0.2:/opt/rocks/mysql/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/bowtie/bowtie-0.12.7:/home/fengyuzhe/.aspera/connect/bin:/home/fengyuzhe/01.Program/02.software/miniconda3/bin:/home/fengyuzhe/01.Program/02.software/mothur/blast/bin:/home/fengyuzhe/01.Program/02.software/mothur:/home/fengyuzhe/01.Program/02.software/Binning:/mnt/lustre/user/fengyuzhe/01.Program/02.software/perlbrew/perls/perl-5.10.1/bin:/mnt/lustre/user/fengyuzhe/01.Program/02.software/perlbrew/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/sratoolkit.2.8.2-1-centos_linux64/bin:/mnt/lustre/user/fengyuzhe/01.Program/02.software/miniconda2/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/mothur/mothur/blast/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/mothur/mothur:~/.local/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/RepeatMasker:/drigen/BioSoftA/vcftools/vcftools_0.1.10/install/bin:/drigen/BioSoftB/exome_pipeline/shenyulanTest/software/tabix-0.2.6:/drigen/BioSoftB/exome_pipeline/annovar:/drigen/BioSoftA/perl/5.16.3/install/bin:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/sun-ct/bin:/opt/blc/genome/bin:/share/raid1/genome/bin:/share/raid1/genome/bin:/opt/blc/genome/bin:/opt/blc/genome/bin:opt/blc/self-software/bin:/opt/gridengine/lib/lx26-amd64:/opt/gridengine/lib/lx26-amd64:/usr/lib/oracle/11.1.0.1/client64/lib:/drigen/BioSoftA/R/2.15.3/install/bin:/drigen/BioSoftB/exome_pipeline/software/soap2.21release:/mnt/lustre/user/fengyuzhe/01.Program/02.software/perlbrew/bin:/mnt/lustre/user/fengyuzhe/01.Program/02.software/perlbrew/perls/perl-5.10.1/bin:/opt/gridengine/bin:/opt/gridengine/bin/lx-amd64:/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/java/latest/bin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/drigen/BioSoftA/samtools/samtools-0.1.19/install/bin:/drigen/BioSoftA/vcftools/vcftools_0.1.10/install/lib/perl5:/drigen/BioSoftB/exome_pipeline/shenyulanTest/software/plink-1.07-i686:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/FastQC:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/hmmer-3.1b2-linux-intel-x86_64/software/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/MetaGenome/scriptsForHumann2/microbiome_helper:/home/fengyuzhe/bin:/drigen/BioSoftA/samtools/samtools-0.1.19/install/bin:/drigen/BioSoftA/vcftools/vcftools_0.1.10/install/lib/perl5:/drigen/BioSoftB/exome_pipeline/shenyulanTest/software/plink-1.07-i686:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/FastQC:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/hmmer-3.1b2-linux-intel-x86_64/software/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/MetaGenome/scriptsForHumann2/microbiome_helper:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/VarDict:/drigen/BioSoftA/samtools/samtools-0.1.19/install/bin:/drigen/BioSoftA/vcftools/vcftools_0.1.10/install/lib/perl5:/drigen/BioSoftB/exome_pipeline/shenyulanTest/software/plink-1.07-i686:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/FastQC:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/hmmer-3.1b2-linux-intel-x86_64/software/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/MetaGenome/scriptsForHumann2/microbiome_helper:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/VarDict:/drigen/BioSoftA/samtools/samtools-0.1.19/install/bin:/drigen/BioSoftA/vcftools/vcftools_0.1.10/install/lib/perl5:/drigen/BioSoftB/exome_pipeline/shenyulanTest/software/plink-1.07-i686:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/FastQC:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/hmmer-3.1b2-linux-intel-x86_64/software/bin:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/MetaGenome/scriptsForHumann2/microbiome_helper:/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/VarDict
PWD=/home/fengyuzhe/01.Program/02.software/VarDictJava
JAVA_HOME=/home/fengyuzhe/01.Program/02.software/miniconda3/bin

原作者：
Yes, I think it is better to update JAVA_HOME to /home/fengyuzhe/01.Program/02.software/miniconda3/, reload bash and try to run build.
There is also a lot of paths to the old java version in PATH variable and it can be a problem in some cases, so perhaps you have to clean your .bashrc a little from old java versions if the previous doesn't help...
我：
yes, thank you very much,

It has been settled

=========================================
$./gradlew clean installDist
Starting a Gradle Daemon (subsequent builds will be faster)

BUILD SUCCESSFUL in 20s
5 actionable tasks: 5 executed
=========================================

export JAVA_HOME="/home/fengyuzhe/01.Program/02.software/miniconda3" 而不是：export JAVA_HOME="/home/fengyuzhe/01.Program/02.software/miniconda3/bin"

因为JAVA_HOME 目录下应该包含 bin, lib，include等各种目录， 而bin下面只包括可执行文件，不包括库文件，头文件。
详细的交流记录：
https://github.com/AstraZeneca-NGS/VarDictJava/issues/233#event-2393462487
我以为只是邮件往返，想不到邮件同时反映到了github的issue上面。

总结起来：
1. 不要用部署在lustre这种mounted硬盘上，用系统自己的盘，比如/home/fengyuzhe/。
2. Java版本要是1.8以上。 但假如你java -version 发现版本没问题，那么是JAVA_HOME出了问题。
3. 就要在~/.bashrc中修改JAVA_HOME。
   export JAVA_HOME="/home/fengyuzhe/01.Program/02.software/miniconda3" 而不是：export JAVA_HOME="/home/fengyuzhe/01.Program/02.software/miniconda3/bin"

我测试过了，在lustre盘上（/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/VarDictJava），即便是修改了JAVA_HOME，也是不行的。
 

最终安装成功，在这个目录下可以找到：

/home/fengyuzhe/01.Program/02.software/VarDictJava/build/install/VarDict/

使用教程在这里：

https://github.com/AstraZeneca-NGS/VarDictJava

安装好之后，可以将build/install/VarDict拷到自己习惯存放的地方，当然，就在原安装目录也完全没问题。
我将其拷贝到这里：
/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/VarDictJava/build/install/VarDict

 

安装后的使用

我在使用VarDict的过程中，始终出现一个问题。

直接在节点上运行，没有问题。

但如果用qsub的方式运行，就始终报错：

Exception in thread "main" java.lang.UnsupportedClassVersionError: com/astrazeneca/vardict/Main : Unsupported major.minor version 52.0
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
        at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
 

 最后想起了

JAVA_HOME的问题，

在shell脚本中添加了：

export JAVA_HOME=/mnt/lustre/user/wubin/01.Program/Scripts/02.software/jdk1.8.0_221

这非常重要，虽然这一行代码我已经放进了 “~/.bashrc”， 直接运行的时候没问题，但qsub的时候“JAVA_HOME”不会被传递给计算节点。

其实可以测试一下： 

$cat test.java_home.sh
#!/bin/sh
#$ -S /bin/sh

echo $JAVA_HOME

$sh test.java_home.sh
得到：
/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/jdk1.8.0_221

 

$ qsub -cwd -V -q genelab.q -pe smp 7 -l h_vmem=60G -e test.java_home.sh.e -o test.java_home.sh.o test.java_home.sh
Your job 590895 ("test.java_home.sh") has been submitted
[wubin@login2 /mnt/lustre/user/fengyuzhe/03.Clinical_Data/11.PanCancer/02.Somatic/sh.e.o/patient_name_probe]
$cat test.java_home.sh.o
/usr/java/latest

可以看出，当投递任务的时候，JAVA_HOME被改回了系统默认的：/usr/java/latest

而该目录下的java： /usr/java/latest/bin/java -version   

$/usr/java/latest/bin/java -version
java version "1.7.0_51"
Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)

 

最终正确的代码如下：

#!/bin/sh
#$ -S /bin/sh

#https://github.com/AstraZeneca-NGS/VarDictJava
export PATH="/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/VarDictJava/build/install/VarDict/bin":$PATH
#export PATH="/home/fengyuzhe/01.Program/02.software/VarDictJava/build/install/VarDict/bin":$PATH
export JAVA_HOME=/mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/jdk1.8.0_221
echo -n "Start: ";date +%Y-%m-%d%t%H:%M:%S
perl /mnt/lustre/user/fengyuzhe/01.Program/Scripts/01.script/GeneLab/CheckStepNormalTermination.pl /mnt/lustre/user/fengyuzhe/03.Clinical_Data/11.PanCancer/01.Germline/sh.e.o/patient-normal_Name_PROBE/R02.BqsrApply.patient-normal_Name_PROBE.sh --standardOut End --standardError error

AF_THR="0.01" # minimum allele frequency
VarDict -G /mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/GATK/fasta_index/hg19.fa -f $AF_THR -N patient_Name_PROBE -b "/mnt/lustre/user/fengyuzhe/03.Clinical_Data/11.PanCancer/02.Somatic/02.SortMarkdupBqsrApply/patient_Name_PROBE/patient_Name_PROBE.marked_duplicates.bam|/mnt/lustre/user/fengyuzhe/03.Clinical_Data/11.PanCancer/01.Germline/02.SortMarkdupBqsrApply/patient-normal_Name_PROBE/patient-normal_Name_PROBE.marked_duplicates.bam" -c 1 -S 2 -E 3 -g 4 -th 6 /mnt/lustre/user/fengyuzhe/01.Program/Scripts/02.software/GATK/bed/test/PROBE.flank100.bed|testsomatic.R |var2vcf_paired.pl -N "patient_Name_PROBE|patient-normal_Name_PROBE" -f $AF_THR >/mnt/lustre/user/fengyuzhe/03.Clinical_Data/11.PanCancer/02.Somatic/03.MuTect2/patient_Name_PROBE/patient_Name_PROBE.vardict.markdup_bam.thread6.vcf
echo -n "End: ";date +%Y-%m-%d%t%H:%M:%S