Hello
I would like to visualize the tracks of my tophat accepted hits bam file. I ran my first sample that was ~10,000,000 reads and it could be visualized in both Trackster and the UCSC genome browser. When I tried to visualize my other samples (which ranged from 15,000,000 to 35,000,000 reads) it won't show up in trackster because of an indexing error. When I ran Picard statistics on the tophat accepted hits bam output, I see that there was successful alignment of ~90% of the reads. Since I have one sample that works, I am not sure how to address the issue.
Here's the error I get from Trackster when I try to visualize the samples:
*** glibc detected *** python: double free or corruption (!prev): 0x0000000000ff02b0 ***
======= Backtrace: =========
/lib/libc.so.6(+0x71ad6)[0x7ff6561f7ad6]
/lib/libc.so.6(cfree+0x6c)[0x7ff6561fc84c]
/lib/libc.so.6(fclose+0x14d)[0x7ff6561e8a1d]
/galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so(bam_index_load_literal+0x37)[0x7ff655cdbb17]
/galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so(+0x6e838)[0x7ff655cc7838]
python(PyObject_Call+0x47)[0x41ef47]
python(PyEval_CallObjectWithKeywords+0x43)[0x4a1a53]
/galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so(+0x52a44)[0x7ff655caba44]
python[0x46f0a3]
python(PyObject_Call+0x47)[0x41ef47]
python(PyEval_EvalFrameEx+0x4878)[0x4a72b8]
python(PyEval_EvalCodeEx+0x911)[0x4a95c1]
python(PyEval_EvalFrameEx+0x4d12)[0x4a7752]
python(PyEval_EvalCodeEx+0x911)[0x4a95c1]
python(PyEval_EvalCode+0x32)[0x4a9692]
python(PyRun_FileExFlags+0x13e)[0x4c98be]
python(PyRun_SimpleFileExFlags+0xd4)[0x4c9ad4]
python(Py_Main+0x9ed)[0x41a6bd]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7ff6561a4c4d]
python[0x4198d9]
======= Memory map: ========
00400000-0061d000 r-xp 00000000 fe:00 715090 /usr/bin/python2.6
0081d000-0087f000 rw-p 0021d000 fe:00 715090 /usr/bin/python2.6
0087f000-0088e000 rw-p 00000000 00:00 0
00d1a000-0109a000 rw-p 00000000 00:00 0 [heap]
7ff650000000-7ff650021000 rw-p 00000000 00:00 0
7ff650021000-7ff654000000 ---p 00000000 00:00 0
7ff6556ed000-7ff655702000 r-xp 00000000 fe:00 1512749 /lib/libgcc_s.so.1
7ff655702000-7ff655902000 ---p 00015000 fe:00 1512749 /lib/libgcc_s.so.1
7ff655902000-7ff655903000 rw-p 00015000 fe:00 1512749 /lib/libgcc_s.so.1
7ff655903000-7ff655933000 r-xp 00000000 00:13 1154848 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/ctabix.so
7ff655933000-7ff655a32000 ---p 00030000 00:13 1154848 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/ctabix.so
7ff655a32000-7ff655a37000 rw-p 0002f000 00:13 1154848 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/ctabix.so
7ff655a37000-7ff655a39000 rw-p 00000000 00:00 0
7ff655a39000-7ff655a55000 r-xp 00000000 fe:00 738300 /usr/lib/python2.6/lib-dynload/_ctypes.so
7ff655a55000-7ff655c55000 ---p 0001c000 fe:00 738300 /usr/lib/python2.6/lib-dynload/_ctypes.so
7ff655c55000-7ff655c59000 rw-p 0001c000 fe:00 738300 /usr/lib/python2.6/lib-dynload/_ctypes.so
7ff655c59000-7ff655d29000 r-xp 00000000 00:13 1154847 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so
7ff655d29000-7ff655e29000 ---p 000d0000 00:13 1154847 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so
7ff655e29000-7ff655e39000 rw-p 000d0000 00:13 1154847 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so
7ff655e39000-7ff655ec0000 rw-p 00000000 00:00 0
7ff655fc0000-7ff656185000 rw-p 00000000 00:00 0
7ff656186000-7ff6562de000 r-xp 00000000 fe:00 1514734 /lib/libc-2.11.2.so
7ff6562de000-7ff6564dd000 ---p 00158000 fe:00 1514734 /lib/libc-2.11.2.so
7ff6564dd000-7ff6564e1000 r--p 00157000 fe:00 1514734 /lib/libc-2.11.2.so
7ff6564e1000-7ff6564e2000 rw-p 0015b000 fe:00 1514734 /lib/libc-2.11.2.so
7ff6564e2000-7ff6564e7000 rw-p 00000000 00:00 0
7ff6564e7000-7ff656567000 r-xp 00000000 fe:00 1514738 /lib/libm-2.11.2.so
7ff656567000-7ff656767000 ---p 00080000 fe:00 1514738 /lib/libm-2.11.2.so
7ff656767000-7ff656768000 r--p 00080000 fe:00 1514738 /lib/libm-2.11.2.so
7ff656768000-7ff656769000 rw-p 00081000 fe:00 1514738 /lib/libm-2.11.2.so
7ff656769000-7ff656780000 r-xp 00000000 fe:00 713314 /usr/lib/libz.so.1.2.3.4
7ff656780000-7ff65697f000 ---p 00017000 fe:00 713314 /usr/lib/libz.so.1.2.3.4
7ff65697f000-7ff656980000 rw-p 00016000 fe:00 713314 /usr/lib/libz.so.1.2.3.4
7ff656980000-7ff656af5000 r-xp 00000000 fe:00 713850 /usr/lib/libcrypto.so.0.9.8
7ff656af5000-7ff656cf5000 ---p 00175000 fe:00 713850 /usr/lib/libcrypto.so.0.9.8
7ff656cf5000-7ff656d1d000 rw-p 00175000 fe:00 713850 /usr/lib/libcrypto.so.0.9.8
7ff656d1d000-7ff656d21000 rw-p 00000000 00:00 0
7ff656d21000-7ff656d70000 r-xp 00000000 fe:00 713852 /usr/lib/libssl.so.0.9.8
7ff656d70000-7ff656f6f000 ---p 0004f000 fe:00 713852 /usr/lib/libssl.so.0.9.8
7ff656f6f000-7ff656f76000 rw-p 0004e000 fe:00 713852 /usr/lib/libssl.so.0.9.8
7ff656f76000-7ff656f78000 r-xp 00000000 fe:00 1514753 /lib/libutil-2.11.2.so
7ff656f78000-7ff657177000 ---p 00002000 fe:00 1514753 /lib/libutil-2.11.2.so
7ff657177000-7ff657178000 r--p 00001000 fe:00 1514753 /lib/libutil-2.11.2.so
7ff657178000-7ff657179000 rw-p 00002000 fe:00 1514753 /lib/libutil-2.11.2.so
7ff657179000-7ff65717b000 r-xp 00000000 fe:00 1514737 /lib/libdl-2.11.2.so
7ff65717b000-7ff65737b000 ---p 00002000 fe:00 1514737 /lib/libdl-2.11.2.so
7ff65737b000-7ff65737c000 r--p 00002000 fe:00 1514737 /lib/libdl-2.11.2.so
7ff65737c000-7ff65737d000 rw-p 00003000 fe:00 1514737 /lib/libdl-2.11.2.so
7ff65737d000-7ff657394000 r-xp 00000000 fe:00 1514748 /lib/libpthread-2.11.2.so
7ff657394000-7ff657593000 ---p 00017000 fe:00 1514748 /lib/libpthread-2.11.2.so
7ff657593000-7ff657594000 r--p 00016000 fe:00 1514748 /lib/libpthread-2.11.2.so
7ff657594000-7ff657595000 rw-p 00017000 fe:00 1514748 /lib/libpthread-2.11.2.so
7ff657595000-7ff657599000 rw-p 00000000 00:00 0
7ff657599000-7ff6575b7000 r-xp 00000000 fe:00 1514704 /lib/ld-2.11.2.so
7ff6575ec000-7ff65762d000 rw-p 00000000 00:00 0
7ff65762e000-7ff6576f1000 rw-p 00000000 00:00 0
7ff657723000-7ff6577aa000 rw-p 00000000 00:00 0
7ff6577b1000-7ff6577b2000 rw-p 00000000 00:00 0
7ff6577b2000-7ff6577b3000 rwxp 00000000 00:00 0
7ff6577b3000-7ff6577b6000 rw-p 00000000 00:00 0
7ff6577b6000-7ff6577b7000 r--p 0001d000 fe:00 1514704 /lib/ld-2.11.2.so
7ff6577b7000-7ff6577b8000 rw-p 0001e000 fe:00 1514704 /lib/ld-2.11.2.so
7ff6577b8000-7ff6577b9000 rw-p 00000000 00:00 0
7fffc7e81000-7fffc7ea2000 rw-p 00000000 00:00 0 [stack]
7fffc7fff000-7fffc8000000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted
--
Erin Shanle
Graduate Research Assistant
Molecular and Environmental Toxicology
425 McArdle Laboratory for Cancer Research
1400 University Ave
Madison, WI 53706
608 262 9834
shanle@wisc.edu