Entering edit mode
10.1 years ago
zengtony743
▴
80
I am sorry to post this again separately since i am not quite sure if this is the computer issue or the issue from the tools. Anyone has this kind of experience?
[xxx@qlogin4 dist]$ java -jar vcffilterjs.jar
Exception in thread "main" java.lang.NoClassDefFoundError: net/sf/samtools/util/BlockCompressedOutputStream
at java.lang.Class.getDeclaredMethods0(Native Method)
at java.lang.Class.privateGetDeclaredMethods(Class.java:2531)
at java.lang.Class.getMethod0(Class.java:2774)
at java.lang.Class.getMethod(Class.java:1663)
at sun.launcher.LauncherHelper.getMainMethod(LauncherHelper.java:494)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:486)
Caused by: java.lang.ClassNotFoundException: net.sf.samtools.util.BlockCompressedOutputStream
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
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)
... 6 more
I wrote this tool.
You should better use https://github.com/lindenb/jvarkit/issues
it's not correctly compiled. Did you follow: https://github.com/lindenb/jvarkit/wiki/Compilation ?
Furthermore, you're using an old code. The path should be
htsjdk/samtools/util/BlockCompressedOutputStream& notnet/sf/samtools/util/BlockCompressedOutputStreamJust stumbled upon your page on the usage in Github and was wondering if I should tag you in here :)
Looks like a possible dependency issue. Maybe a required jar file is missing?
Thank you, Pierre and Ram.. actually I do use a old code that I used 8 month ago.. so according to your suggestions. I need to re-install and do the right compilation by linkers you sent to me. Am I right?
Since I am using old code,, so that mean my previous command java -jar dist/vcffilterjs.jar -f script.js 280control.vcf > 84U1.vcf & need to change too?
Thank you,
yes, reinstall, I won't/can't help with an old version.
Pierre,
Since I do not have permission to install jvarkit under cluster but by staff of computer center.. for me, I want to use script.js that you wrote before and do filter within one VCF file which include many samples. followings are a list that all the tools in the jvarkit and IT people helped me scripting the install but some applications failed to install...Since this new javrkit package seems totally different from old version. For me, if I want to use
java -jar dist/vcffilterjs.jar -f script.js 280control.vcf > 84U1.vcfwhich is the application that i need to use and how to use it? ( https://www.biostars.org/p/88921/ )I don't think you'd need
sudoprivileges to installgitoranton the HPC. I don't see why using jvarkit downloaded to a user directory should be a problem.It's still
vcffilterjsbut you need to download the latest updated version.We installed the updated version when I ran the command, it shows as this
are you sure about '-Xmx15g !' ? that must be a huge VCF !!! this tool uses streaming operation, memory shouldn't be a problem.
there must be some quotes in your command line that you don't show us: java can get the only option
-jar. Let me show you a normal message:see ? to trailing words after "Unrecognized option: -HelloWorld"
Pierre, It works this time finally just because of lack of enough memory. You are right, my VCF is really huge, I set it as
-Xmx45gthen it worksThank you :)
Sorry I posted the question as an answer by an accident!
The problem is with your demand for 15G of RAM. Your login or compute node config might not allow that limit and so is unable to create the JVM. Try a reasonable limit, such as 4G. The command should be:
Thank you, RamRS, see the msg above :)
That was a twist I did not see coming! More memory, not less, eh? Nice!