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Troubleshooting
My script submitted but I can't see any error files.
Do you have a folder in the logFiles folder with your username.
_What are these temporary bam files and where did they come from? _
The presence of files with file ending such as .bam.tmp.0000.bam, or with the filename core indicate an out of memory (OOM) error at some point in the pipeline. You will need to re run the command either requesting more memory for the affected programme or on a higher memory node.
My sample has aligned but the job was killed during the post filtering steps.
A. If your sample has a lot of reads, you may run into memory issues. The tell tale sign is the presence of tmp bam files e.g. *.bam.tmp.0000.bam. We observed this happened if > 500,000,000 paired reads. Try to run these samples on higher memory nodes.