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
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