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An error when running PathSeqFilterSpark
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 \
Then running PathSeqFilterSpark:
/home/jw380/tools/GATK4/gatk-184.108.40.206/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 \
--filter-bwa-image hg38.fa.img \
--filter-metrics FZ-97_metrics.txt \