[Biopython] [Samtools-help] Segmentation fault
Mic
mictadlo at gmail.com
Tue Oct 18 23:12:03 UTC 2011
I run it now on my Laptop (Ubuntu 11.04 x64) and now I can see the core
file:
$ ulimit -c unlimited
$ python subsetBAM-P.py --BAM ex1.bam -f ex1.fa -o new.bam
Segmentation fault (core dumped)
$ file core
core: ELF 64-bit LSB core file x86-64, version 1 (SYSV), SVR4-style, from
'python subsetBAM-P.py --BAM ex1.bam -f ex1.fa -o new.bam'
$ gdb /usr/bin/python ./core
GNU gdb (Ubuntu/Linaro 7.2-1ubuntu11) 7.2
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-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /usr/bin/python...(no debugging symbols found)...done.
[New Thread 2748]
warning: Can't read pathname for load map: Input/output error.
Reading symbols from /lib/x86_64-linux-gnu/libpthread.so.0...(no debugging
symbols found)...done.
Loaded symbols for /lib/x86_64-linux-gnu/libpthread.so.0
Reading symbols from /lib/x86_64-linux-gnu/libdl.so.2...(no debugging
symbols found)...done.
Loaded symbols for /lib/x86_64-linux-gnu/libdl.so.2
Reading symbols from /lib/x86_64-linux-gnu/libutil.so.1...(no debugging
symbols found)...done.
Loaded symbols for /lib/x86_64-linux-gnu/libutil.so.1
Reading symbols from /lib/libssl.so.0.9.8...(no debugging symbols
found)...done.
Loaded symbols for /lib/libssl.so.0.9.8
Reading symbols from /lib/libcrypto.so.0.9.8...(no debugging symbols
found)...done.
Loaded symbols for /lib/libcrypto.so.0.9.8
Reading symbols from /lib/x86_64-linux-gnu/libz.so.1...(no debugging symbols
found)...done.
Loaded symbols for /lib/x86_64-linux-gnu/libz.so.1
Reading symbols from /lib/x86_64-linux-gnu/libm.so.6...(no debugging symbols
found)...done.
Loaded symbols for /lib/x86_64-linux-gnu/libm.so.6
Reading symbols from /lib/x86_64-linux-gnu/libc.so.6...(no debugging symbols
found)...done.
Loaded symbols for /lib/x86_64-linux-gnu/libc.so.6
Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols
found)...done.
Loaded symbols for /lib64/ld-linux-x86-64.so.2
Reading symbols from /usr/lib/python2.7/lib-dynload/_heapq.so...(no
debugging symbols found)...done.
Loaded symbols for /usr/lib/python2.7/lib-dynload/_heapq.so
Reading symbols from /usr/lib/python2.7/lib-dynload/_elementtree.so...(no
debugging symbols found)...done.
Loaded symbols for /usr/lib/python2.7/lib-dynload/_elementtree.so
Reading symbols from /lib/x86_64-linux-gnu/libexpat.so.1...(no debugging
symbols found)...done.
Loaded symbols for /lib/x86_64-linux-gnu/libexpat.so.1
Reading symbols from /usr/lib/python2.7/lib-dynload/pyexpat.so...(no
debugging symbols found)...done.
Loaded symbols for /usr/lib/python2.7/lib-dynload/pyexpat.so
Reading symbols from
/home/mic/apps/pymodules/lib/python2.7/site-packages/pysam-0.5-py2.7-linux-x86_64.egg/csamtools.so...done.
Loaded symbols for
/home/mic/apps/pymodules/lib/python2.7/site-packages/pysam-0.5-py2.7-linux-x86_64.egg/csamtools.so
Reading symbols from /usr/lib/python2.7/lib-dynload/_ctypes.so...(no
debugging symbols found)...done.
Loaded symbols for /usr/lib/python2.7/lib-dynload/_ctypes.so
Reading symbols from
/home/mic/apps/pymodules/lib/python2.7/site-packages/pysam-0.5-py2.7-linux-x86_64.egg/ctabix.so...done.
Loaded symbols for
/home/mic/apps/pymodules/lib/python2.7/site-packages/pysam-0.5-py2.7-linux-x86_64.egg/ctabix.so
Reading symbols from
/home/mic/apps/pymodules/lib/python2.7/site-packages/pysam-0.5-py2.7-linux-x86_64.egg/TabProxies.so...done.
Loaded symbols for
/home/mic/apps/pymodules/lib/python2.7/site-packages/pysam-0.5-py2.7-linux-x86_64.egg/TabProxies.so
Reading symbols from /usr/lib/python2.7/lib-dynload/_io.so...(no debugging
symbols found)...done.
Loaded symbols for /usr/lib/python2.7/lib-dynload/_io.so
Reading symbols from
/home/mic/apps/pymodules/lib/python2.7/site-packages/pysam-0.5-py2.7-linux-x86_64.egg/cvcf.so...done.
Loaded symbols for
/home/mic/apps/pymodules/lib/python2.7/site-packages/pysam-0.5-py2.7-linux-x86_64.egg/cvcf.so
Reading symbols from
/usr/lib/python2.7/lib-dynload/_multiprocessing.so...(no debugging symbols
found)...done.
Loaded symbols for /usr/lib/python2.7/lib-dynload/_multiprocessing.so
Reading symbols from /usr/lib/pymodules/python2.7/Bio/Nexus/cnexus.so...(no
debugging symbols found)...done.
Loaded symbols for /usr/lib/pymodules/python2.7/Bio/Nexus/cnexus.so
Core was generated by `python subsetBAM-P.py --BAM ex1.bam -f ex1.fa -o
new.bam'.
Program terminated with signal 11, Segmentation fault.
#0 __pyx_pf_9csamtools_11AlignedRead_5qname___get__ (o=0x164e138,
x=<value optimized out>) at pysam/csamtools.c:18123
18123 if (__pyx_t_1) {
(gdb)
(gdb) where
#0 __pyx_pf_9csamtools_11AlignedRead_5qname___get__ (o=0x164e138,
x=<value optimized out>) at pysam/csamtools.c:18123
#1 __pyx_getprop_9csamtools_11AlignedRead_qname (o=0x164e138,
x=<value optimized out>) at pysam/csamtools.c:30806
#2 0x0000000000479804 in ?? ()
#3 0x00007f187dbabc65 in __pyx_pf_9csamtools_11AlignedRead___str__ (
__pyx_v_self=0x164e138) at pysam/csamtools.c:17687
#4 0x0000000000479eac in _PyObject_Str ()
#5 0x0000000000479f8a in PyObject_Str ()
#6 0x00000000004d390c in ?? ()
#7 0x00000000004cd2d1 in PyFile_WriteObject ()
#8 0x000000000049909d in PyEval_EvalFrameEx ()
#9 0x000000000049d325 in PyEval_EvalCodeEx ()
#10 0x00000000004ecb02 in PyEval_EvalCode ()
#11 0x00000000004fdc74 in ?? ()
#12 0x000000000042c182 in PyRun_FileExFlags ()
#13 0x000000000042cb4a in PyRun_SimpleFileExFlags ()
#14 0x0000000000418c9e in Py_Main ()
#15 0x00007f187ed7aeff in __libc_start_main ()
from /lib/x86_64-linux-gnu/libc.so.6
#16 0x00000000004c62b1 in _start ()
(gdb)
(gdb) bt full
#0 __pyx_pf_9csamtools_11AlignedRead_5qname___get__ (o=0x164e138,
x=<value optimized out>) at pysam/csamtools.c:18123
__pyx_v_src = 0x0
__pyx_t_2 = 0x0
__pyx_frame = 0x0
__pyx_r = 0x0
__pyx_t_1 = <value optimized out>
__Pyx_use_tracing = 0
__pyx_frame_code = 0x0
#1 __pyx_getprop_9csamtools_11AlignedRead_qname (o=0x164e138,
x=<value optimized out>) at pysam/csamtools.c:30806
No locals.
#2 0x0000000000479804 in ?? ()
No symbol table info available.
#3 0x00007f187dbabc65 in __pyx_pf_9csamtools_11AlignedRead___str__ (
__pyx_v_self=0x164e138) at pysam/csamtools.c:17687
__pyx_r = 0x0
__pyx_t_1 = 0x1e4fb90
__pyx_t_2 = 0x0
__pyx_t_3 = 0x0
__pyx_t_4 = 0x0
---Type <return> to continue, or q <return> to quit---
__pyx_t_5 = 0x0
__pyx_t_6 = 0x0
__pyx_t_7 = 0x0
__pyx_t_8 = 0x0
__pyx_t_9 = 0x0
__pyx_t_10 = 0x0
__pyx_t_11 = 0x0
__pyx_t_12 = 0x0
__pyx_t_13 = 0x0
__pyx_t_14 = 0x0
__pyx_frame_code = 0x0
__pyx_frame = 0x0
__Pyx_use_tracing = 0
#4 0x0000000000479eac in _PyObject_Str ()
No symbol table info available.
#5 0x0000000000479f8a in PyObject_Str ()
No symbol table info available.
#6 0x00000000004d390c in ?? ()
No symbol table info available.
#7 0x00000000004cd2d1 in PyFile_WriteObject ()
No symbol table info available.
---Type <return> to continue, or q <return> to quit---
#8 0x000000000049909d in PyEval_EvalFrameEx ()
No symbol table info available.
#9 0x000000000049d325 in PyEval_EvalCodeEx ()
No symbol table info available.
#10 0x00000000004ecb02 in PyEval_EvalCode ()
No symbol table info available.
#11 0x00000000004fdc74 in ?? ()
No symbol table info available.
#12 0x000000000042c182 in PyRun_FileExFlags ()
No symbol table info available.
#13 0x000000000042cb4a in PyRun_SimpleFileExFlags ()
No symbol table info available.
#14 0x0000000000418c9e in Py_Main ()
No symbol table info available.
#15 0x00007f187ed7aeff in __libc_start_main ()
from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#16 0x00000000004c62b1 in _start ()
No symbol table info available.
(gdb) quit
$ ulimit -a
core file size (blocks, -c) unlimited
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 20
file size (blocks, -f) unlimited
pending signals (-i) 16382
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) unlimited
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
Thank you in advance.
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