On 16 Feb 2016, at 23:22, Friedman, Ryan <[email protected]> wrote: > The entire pipeline works fine up until rmdup where it immediately results in > a segmentation fault. > > What's particularly interesting is that this seg fault only occurs in some > files. I originally thought this had something to do with size or memory > allocation, since rmdup worked fine with RNA seq data but not with this > genome seq data. However, the seg fault still occurred even when I allocated > more memory. > > Furthermore, I think this might be a bug. The lab group I work with recently > switched to a new cluster system. I run into the seg fault on the new > cluster, which is running samtools 1.3
Thanks for tracking this down in gdb. This is new code that was written to reactivate the old rmdup command, so may indeed contain a new bug. To reproduce this it would be good to see the @RG header it was looking at at the time. If you can share them, please email me off-list the headers from one of the files that caused a segfault. John -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
