On Mon, Jul 06, 2015 at 09:29:26AM +0100, Albert Vilella wrote: > I am just reporting on something I saw over the weekend. A samtools > sort command executed on Friday was still running this morning on a > file that should have taken a relatively short time to sort. > > The input file is about 241M, and this morning, samtools-0.1.18 sort > was producing a file that was 1000x bigger, 236G and growing when I > killed it.
Wow! What was in the file it was creating? Any clues as to what the bulk was? Of more interest is whether this same input file still causes problems with the newest Samtools. If not then it's unlikely to get fixed, at least officially. (Some linux releases may patch it if there is a fix for the 0.1.19+ I guess.) James -- James Bonfield ([email protected]) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. -- 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. ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
