Erin, This was due to a temporary issue that has been fixed. However, you'll need to copy the problematic datasets and use the new copy for visualization. To copy datasets, use History Options --> Copy Datasets; you can select the source history as your target history to copy datasets within a history. Thanks, J. On Jan 20, 2012, at 9:57 AM, Erin Shanle wrote:

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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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