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An error when running PathSeqFilterSpark

Dear GATKer,
I just run PathSeqFilterSpark using the command, but there is an error and I had no idea about that. I uploaded the log file, could you please help me have a check?

I generated an unmapped BAM from raw paired-end fastq files using Picard's FastqToSam as input:
java -Xmx8G -jar /home/jw380/tools/PICARD/picard.jar FastqToSam \
FASTQ=/n/groups/liu/public/Xiaoqi_samples/fastq/FZ-97_R1.fq \
FASTQ2=/n/groups/liu/public/Xiaoqi_samples/fastq/FZ-97_R2.fq \
OUTPUT=FZ-97_fastqtosam.bam \
SAMPLE_NAME=FZ-97

Then running PathSeqFilterSpark:
/home/jw380/tools/GATK4/gatk-4.0.5.2/gatk PathSeqFilterSpark \
--input /n/groups/liu/jinwang/Lung_samples/TB/gatk/FZ-97_fastqtosam.bam \
--paired-output /n/groups/liu/jinwang/Lung_samples/TB/gatk/FZ-97_reads_paired.bam \
--unpaired-output /n/groups/liu/jinwang/Lung_samples/TB/gatk/FZ-97_reads_unpaired.bam \
--is-host-aligned true \
--kmer-file host_hg38.hss\
--filter-bwa-image hg38.fa.img \
--filter-metrics FZ-97_metrics.txt \

Best,
Jin

Best Answer

  • markwmarkw Cambridge, MA admin
    Accepted Answer

    Hello @JinWang

    Thank you for posting your question to the forums. It looks like your JVM is running out of memory. Try increasing the heap size as described here. You will need at least as much memory as the size of the k-mer file.

Answers

  • markwmarkw Cambridge, MAMember, Broadie, Dev admin
    Accepted Answer

    Hello @JinWang

    Thank you for posting your question to the forums. It looks like your JVM is running out of memory. Try increasing the heap size as described here. You will need at least as much memory as the size of the k-mer file.

  • JinWangJinWang Member

    Hi markw,
    Thanks for your answer. This really solved my problem and now I can smoothly run the total PathSeqPipeline. Thank you very much!

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