Hi Ian, sorry for the delay in responding (this apology applies to the many other unanswered emails as well). There has been lot of development lately, can you please try with the latest version?
Cheers, Petr On Sun, 2014-08-03 at 16:20 -0700, Ian Fiddes wrote: > Hi All, > > > I am running into a segmentation fault when running mpileup. The sam > file on its own works, but when a reference fasta is used it > segfaults. The example files used in this test can be found at The > example files can be found > athttp://hgwdev.soe.ucsc.edu/~ifiddes/samtools_bug/ > > > Here is the gdb trace: > > > -bash-4.1$ gdb samtools > > GNU gdb (GDB) Red Hat Enterprise Linux (7.2-60.el6) > > Copyright (C) 2010 Free Software Foundation, Inc. > > License GPLv3+: GNU GPL version 3 or later > <http://gnu.org/licenses/gpl.html> > > This is free software: you are free to change and redistribute it. > > There is NO WARRANTY, to the extent permitted by law. Type "show > copying" > > and "show warranty" for details. > > This GDB was configured as "x86_64-redhat-linux-gnu". > > For bug reporting instructions, please see: > > <http://www.gnu.org/software/gdb/bugs/>... > > Reading symbols from /cluster/bin/x86_64/samtools...done. > > (gdb) run mpileup -q 0 -uf test.fa example.bam > > ?BCfH??BCFDNA_CS > > example.bam%##samtoolsVersion=0.1.18 (r982:295) > > <mpileup> Set max per-file depth to 8000 > > ??$H?BC#???2GXDP=0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0PL2CXDP=0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0PL2CXDP=0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0PL2AXDP=0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0PL2TXDP=0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0PL2CXDP=0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0PL2AXDP=0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0PL2GXDP=0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0P2AXDP=0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0PL2TXDP=0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0PL > > 2TXDP=0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0PL > > <removed intervening output> > > > Program received signal SIGSEGV, Segmentation fault. > > 0x000000000043f379 in kpa_glocal (_ref=0x65a603 "\002\004\001", > l_ref=5, > > _query=0x65a780 "", l_query=0, iqual=0x65a9f0 "", > c=0x7fffffffdbd0, > > state=0x0, q=0x0) at kprobaln.c:119 > > 119 fi[u+0] = e * bM; fi[u+1] = EI * bI; > > Missing separate debuginfos, use: debuginfo-install > glibc-2.12-1.107.el6.x86_64 ncurses-libs-5.7-3.20090208.el6.x86_64 > zlib-1.2.3-29.el6.x86_64 > > > > > Thanks, > Ian Fiddes > ------------------------------------------------------------------------------ > Want fast and easy access to all the code in your enterprise? Index and > search up to 200,000 lines of code with a free copy of Black Duck > Code Sight - the same software that powers the world's largest code > search on Ohloh, the Black Duck Open Hub! Try it now. > http://p.sf.net/sfu/bds > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help -- 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. ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
