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Random java.io.FileNotFoundException version 2.7-2-g6bda569
We are running into some random weirdness when running jobs using SGE, GATK version 2.7-2-g6bda569, pretty much all GATK tools - but mostly IndelRealigner abd UnifiedGenotyper, we often get the following error:-
ERROR MESSAGE: Couldn't read file /scratch/project/pipelines/novorecal.bam because java.io.FileNotFoundException: /scratch/project/pipelines/novorecal.bam (No such file or directory)
This also happens for supplied reference genomes and vcf files. The GATK tool cant find them.
These "missing" files do exist, and have often even been created by the previous tool/step in the pipeline.
When we re-run the pipeline on a failed sample, it works. So we end up having to re-run our pipeline on the same set of samples multiple times and are beginning to find this very frustrating. These errors seem to be random, I cant find any pattern, and as I mentioned, when we re-run the pipeline on a failed run, it work without a hitch.
Has anyone experienced this? And if so, any recommendations?