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[variation-calling] GATK进行BaseRecalibrator 碱基矫正时报错如何修改

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发表于 2020-8-18 16:10:05 | 显示全部楼层 |阅读模式
我把命令行写进.sh脚本,放服务器后台运行,结果报错:Error: Invalid or corrupt jarfile /share/home/software/CentOS-6/gatk-4.1.5.0/gatk-package-4.1.5.0-local.jar。
但是同样的命令行,无论是软件目录还是数据目录下直接运行,都可以顺利运行。百思不得其解。有知道的朋友麻烦指点一下。shell脚本如下:
/share/home/software/CentOS-6/gatk-4.1.5.0/gatk --java-options "-Xmx20G -Djava.io.tmpdir=/share/home/lvqiang/WES/Result/S2/bam" BaseRecalibrator -R /share/home/lvqiang/WES/resource/hg38/Homo_sapiens_assembly38.fasta -I /share/home/lvqiang/WES/Result/S2/bam/dedup_reads.bam -O /share/home/lvqiang/WES/Result/S2/bam/dedup_reads_recal.table --known-si    tes /share/home/lvqiang/WES/resource/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz --known-sites /share/home/lvqiang/WES/resource/hg38/dbsnp_146.    hg38.vcf.gz --known-sites /share/home/lvqiang/WES/resource/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
我确定GATK安装没有问题,即使绝对路径下运行gatk --list 也没有问题

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