I'm using a couple programs to look at repetitive DNA in mapped reads (bamfiles): genotan and repeatseq. Both programs have publications and are designed to work on bamfiles.
The problem is that I'm getting segmentation faults from both programs on some of the bamfiles I would like to analyze. It's hard to tell for sure why some bamfiles run successfully while others seg fault. There does appear to be a much greater tendency to seg fault on any bamfile created with bwa. Im wondering if there are any formatting differences between bwa and bowtie2 mapped bamfiles and if there is a way to repair the files that fail without remapping. Perhaps its a whitespace issue or special character issue. Debugging the programs myself is probably unfeasible so Im looking for any other solution, Thanks
Try running your script with providing more memory.Segmentation faults could be because of insufficient memory.