HaplotypeCaller Step for Whole Genome Sequencing Data

Question

[mostafarafiepour]

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

[WouterDeCoster]

This question might be more appropriate on the GATK support forum

Answer 1

[Ram]

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.

[mostafarafiepour]

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

[Ram]

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