picard报错(Too many open files)

最近使用picard时出现如下报错，记录一下

java.io.FileNotFoundException: (Too many open files)

运行代码如下：

    java -jar picard.jar MarkDuplicates I=L-pool.A10.sort.rg.bam O=L-pool.A10.mark.dup.bam M=L-pool.A10.mark.dup.metrics VALIDATION_STRINGENCY=SILENT

解决办法

增加参数即可MAX_RECORDS_IN_RAM=1000000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000

    java -jar icard.jar MarkDuplicates I=L-pool.A10.sort.rg.bam O=L-pool.A10.mark.dup.bam M=L-pool.A10.mark.dup.metrics VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=1000000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000
posted @ 2020-03-14 14:59  raisok  阅读(723)  评论(0)  编辑  收藏  举报