Yes, it is a mapping to assembled metagenomic contigs which has 6907774 sequences.
On 6/16/15, 3:57 AM, "John Marshall" <j...@sanger.ac.uk> wrote: >On 15 Jun 2015, at 17:46, Lo, Chien-Chi <chien...@lanl.gov> wrote: >> Samtools (v1.2) merge doesn¹t output any file of my two bam file and no >>message throwing out. It just hang there and reserved ~2.0g memory. >>However, 0.1.18 version finish the merging in ~2 mins. >> >> The two sorted bam files are 449M and 448M in size. > >Do your bam files have many many headers? Samtools 1.2 merge could run >for a very long time on such headers on some platforms [1]; thanks to >Nathan Weeks, this problem has been fixed and the next samtools release >should merge such files as fast as 0.1.x samtools. > >Giuseppe Aprea <giuseppe.ap...@gmail.com> wrote previously: >> I am trying to merge 4 sorted bam files with samtools (v 1.2) but I get >>the following error: >> >> 39656 Segmentation fault (core dumped) samtools merge merging.bam >>*.sorted.realigned.nodup.sorted.bam > >Giuseppe's problem appears to be different, and it would indeed be useful >to see a stack trace. > > John > >[1] https://github.com/samtools/samtools/pull/337 > >-- > 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. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
