Question: HaplotypeCaller Step for Whole Genome Sequencing Data
0
gravatar for mostafarafiepour
2.0 years ago by
mostafarafiepour60 wrote:

Hi all,

I have a problem in the HaplotypeCaller Step for Whole Genome Sequencing Data. after run this step i getting the following error massage (In the attached image).Due to two errors created (in the image), the run step begins and remains in this position for more than two days without having an output? any idea what this might be?

Code i run:

java –Xmx64g -jar /home/m.rafiepour222/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar –R /home/m.rafiepour222/GCF_000298355.1_BosGru_v2.0_genomic.fa -T HaplotypeCaller -I /home/m.rafiepour222/SRR3112417/SRR3112417.sort.rmdup.bam -o /home/m.rafiepour222/SRR3112417/SRR3112417.raw.snps.indels.g.vcf

Best Regard

Mostafa

enter image description here

snp • 655 views
ADD COMMENTlink modified 2.0 years ago by RamRS25k • written 2.0 years ago by mostafarafiepour60

This question might be more appropriate on the GATK support forum

ADD REPLYlink written 2.0 years ago by WouterDeCoster43k
0
gravatar for RamRS
2.0 years ago by
RamRS25k
Houston, TX
RamRS25k wrote:

First off, there seems to be a problem with the -Xmx64g argument, which I guess is caused by a copy-paste that uses a different hyphen for the argument than the one needed. Try typing the command instead of copy paste. Also, the error message below gives you a hint:

Please add log4j-core to the classpath

I'd type the command ensuring the right hyphens are used, follow up with a Google search using the above error message, and take it from there.

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by RamRS25k

many thanks for your reply, the log4j-core exactly where to add??

my code: java –Xmx64g -jar /home/m.rafiepour222/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar –R /home/m.rafiepour222/GCF_000298355.1_BosGru_v2.0_genomic.fa -T HaplotypeCaller -I /home/m.rafiepour222/SRR3112417/SRR3112417.sort.rmdup.bam -o /home/m.rafiepour222/SRR3112417/SRR3112417.raw.snps.indels.g.vcf

ADD REPLYlink written 2.0 years ago by mostafarafiepour60

Did you try replacing the hyphen? Tackle log4j later. Adding it to the classpath = adding the location of the jar file to the CLASSPATH environment variable, AFAIK

ADD REPLYlink written 2.0 years ago by RamRS25k
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