I am using GATK intervals(hg19) to parallize the
I am getting the following error whilt trying do start Indel realigner or Base recalibrator step.
ERROR MESSAGE: An error occurred when trying to write the BAM file. Usually this happens when there is not enough space in the directory to which the data is being written (generally the temp directory) or when your system's open file handle limit is too small. To tell Java to use a bigger/better file system use -Djava.io.tmpdir=X on the command line. The exact error was Terminator block not found after closing BGZF file /Somatic/data/b/SHH007/tmp_data/SHH007.reAligned_chr1:125000001-249250621.bam
I did check /tmp. Its not running out of space...