Old problem solved but new one comes...
Here are commands that I used:
java -Xmx45g -jar /hpf/tools/centos6/jvarkit/2014.10.15/dist/vcffilterjs.jar -f script.js allsnp1.vcf > 136F1.vcf &
Here is the script.js (from Pierre)
function accept(ctx)
{
var y,g2;
var sampleList=header.getSampleNamesInOrder();
var g1=ctx.getGenotype("136");
/** ignore non-called */
if(g1== null || ! g1.isCalled() ) return false;
/** loop over the other samples */
for(y=0;y< sampleList.size();++y)
{
g2=ctx.getGenotype( sampleList.get(y) );
if(g2.getSampleName().equals(g1.getSampleName())) continue;
/** ignore non-called */
if(! g2.isCalled() ) continue;
/** is g1==g2 ? */
if( g1.sameGenotype( g2 ) ) return false;
}
/* found no other same genotype */
return true;
}
accept(variant);
the size of output file is small as 26K. here is the output looking like
........
........
.......
....
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##VCFFilterJSCmdLine=-f script.js allsnp1.vcf
##VCFFilterJSVersion=c83f20cde867920870918ee6eb5e5406f554e2bb
##contig=<ID=chr10,length=130694993>
##contig=<ID=chr11,length=122082543>
##contig=<ID=chr12,length=120129022>
##contig=<ID=chr13,length=120421639>
##contig=<ID=chr14,length=124902244>
##contig=<ID=chr15,length=104043685>
##contig=<ID=chr16,length=98207768>
##contig=<ID=chr17,length=94987271>
##contig=<ID=chr18,length=90702639>
##contig=<ID=chr19,length=61431566>
##contig=<ID=chr1,length=195471971>
##contig=<ID=chr2,length=182113224>
##contig=<ID=chr3,length=160039680>
##contig=<ID=chr4,length=156508116>
##contig=<ID=chr5,length=151834684>
##contig=<ID=chr6,length=149736546>
##contig=<ID=chr7,length=145441459>
##contig=<ID=chr8,length=129401213>
##contig=<ID=chr9,length=124595110>
##contig=<ID=chrM,length=16299>
##contig=<ID=chrX,length=171031299>
##contig=<ID=chrY,length=91744698>
##reference=file:///hpf/projects/mjustice/reference/genome.fa
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 111 129_Control 136 137 186 195 196 198 620 752 97 C57B6_control Chol1_592 Crf03_82 Crf04_151 L11J27 L11J74 M1527_280 M1527_305 M1527_84 M895_206 M895_417 M895_419 M895_64 Nur19_1457
But no MORE information after the line of (#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT)
•
written
by
Pierre Lindenbaum
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/ )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!
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.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 ?
Just stumbled upon your page on the usage in Github and was wondering if I should tag you in here :)
Furthermore, you're using an old code. The path should be
htsjdk/samtools/util/BlockCompressedOutputStream& notnet/sf/samtools/util/BlockCompressedOutputStream