Hi Peter Thanks, you are right, it was not the CIGAR string but something to do with the read group code.
Setting -R to tell mpileup ignore the read group fixes it. I did not specifically set a read group when I made these BAM files, perhaps doing this is another workaround. I guess there is still some problem that needs fixing however. Cheers Nick On Fri, Oct 31, 2014 at 12:45 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Hmm, > > Very long CIGAR strings used to cause a crash, they ought now to be > caught and trigger an error: > > https://github.com/samtools/samtools/pull/39 > > Peter > > On Fri, Oct 31, 2014 at 12:38 PM, Nick Loman <n.j.lo...@bham.ac.uk> wrote: > > Latest build of samtools (1.1) mpileup core dumps with the following file > > (produced with latest BWA and samtools on nanopore data) in -g (BCF) or > -v > > (VCF) mode, e.g.. > > > > samtools mpileup -Q 0 -f NC_000913.fna -g Ecoli_R73_2D.bam > > > > I wonder if there is some kind of buffer overflow, e.g. with a long CIGAR > > string. > > > > The file is available here: > > > > http://pathogenomics.bham.ac.uk/filedist/nanopore/Ecoli_R73_2D.bam > > > > Any ideas anyone? > > > > GDB backtrace: > > #0 0x00007ffff6ec1bb9 in __GI_raise (sig=sig@entry=6) at > > ../nptl/sysdeps/unix/sysv/linux/raise.c:56 > > #1 0x00007ffff6ec4fc8 in __GI_abort () at abort.c:89 > > #2 0x0000000000459a1f in skip_aux (s=<optimised out>) at sam.c:1071 > > #3 bam_aux_get (b=<optimised out>, tag=<optimised out>) at sam.c:1087 > > #4 0x0000000000404e9b in group_smpl (ignore_rg=0, plp=0x6b8150, > > n_plp=0x6b8170, fn=0x7fffffffe350, > > n=1, buf=0x7fffffffdc50, sm=0x6b8010, m=0x7fffffffdc30) at > > bam_plcmd.c:198 > > #5 mpileup (conf=<optimised out>, n=1, fn=0x7fffffffe350) at > > bam_plcmd.c:451 > > #6 0x000000000040779c in bam_mpileup (argc=<optimised out>, > argv=<optimised > > out>) > > at bam_plcmd.c:875 > > #7 0x00007ffff6eacec5 in __libc_start_main (main=0x403af0 <main>, > argc=8, > > argv=0x7fffffffe318, > > init=<optimised out>, fini=<optimised out>, rtld_fini=<optimised > out>, > > stack_end=0x7fffffffe308) > > at libc-start.c:287 > > #8 0x0000000000404051 in _start () > > > > Cheers > > > > > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > > Samtools-help mailing list > > Samtools-help@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/samtools-help > > >
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