Hi Nancy, I'm ccing the galaxy-user mailing list as this discussion may be helpful to others. The problem is that your BAM dataset isn't sorted. Galaxy requires that uploaded BAMs be sorted to be useful for most tools and for visualization. You can fix this in two ways: (a) using samtools from the command line and then uploading the sorted file to Galaxy: samtools sort in.bam out_prefix (b) from Galaxy, use tools to convert the BAM to SAM and back again to BAM; the output of the SAM to BAM tool will be sorted. Taking either of these steps will enable visualization in Trackster. Best, J. On Jul 13, 2012, at 5:34 PM, Nancy Au Yeung wrote:
On Fri, Jul 13, 2012 at 2:29 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote: Hi Nancy,
Can you share the history with the problematic dataset(s) with me and I can take a look? Please share the history with me using my email address: jeremy.goecks@emory.edu
Best, J.
On Jul 12, 2012, at 9:07 PM, Nancy Au Yeung wrote:
Hi,
I saw another post regarding trackster error and it seems like this is different. I have tried copying the dataset from the History option, but this same error occurs. See error script below.
Thanks!
Trackster Error
*** glibc detected *** python: double free or corruption (top): 0x0000000001c09370 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x75ab6)[0x7f93fe421ab6] /lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c)[0x7f93fe4267ec] /lib/x86_64-linux-gnu/libc.so.6(fclose+0x14d)[0x7f93fe412a0d] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(bam_index_load_literal+0x37)[0x7f93fdac2ad7] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(+0x6e7f8)[0x7f93fdaae7f8] python(PyObject_Call+0x36)[0x4824c6] python(PyEval_CallObjectWithKeywords+0x36)[0x486086] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(+0x52a04)[0x7f93fda92a04] python[0x482068] python(PyObject_Call+0x36)[0x4824c6] python(PyEval_EvalFrameEx+0x91a)[0x4c5e8a] python(PyEval_EvalCodeEx+0x136)[0x4ccee6] python(PyEval_EvalFrameEx+0x838)[0x4c5da8] python(PyEval_EvalCodeEx+0x136)[0x4ccee6] python(PyRun_FileExFlags+0xe1)[0x577901] python(PyRun_SimpleFileExFlags+0x177)[0x577b37] python(Py_Main+0x6f7)[0x550497] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd)[0x7f93fe3caead] python[0x41dea1] ======= Memory map: ======== 00400000-00672000 r-xp 00000000 fe:00 893421 /usr/bin/python2.7 00871000-00872000 r--p 00271000 fe:00 893421 /usr/bin/python2.7 00872000-008db000 rw-p 00272000 fe:00 893421 /usr/bin/python2.7 008db000-008ed000 rw-p 00000000 00:00 0 0166d000-01c29000 rw-p 00000000 00:00 0 [heap] 7f93f8000000-7f93f8021000 rw-p 00000000 00:00 0 7f93f8021000-7f93fc000000 ---p 00000000 00:00 0 7f93fd6de000-7f93fd70e000 r-xp 00000000 00:18 458639 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/ctabix.so 7f93fd70e000-7f93fd80d000 ---p 00030000 00:18 458639 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/ctabix.so 7f93fd80d000-7f93fd812000 rw-p 0002f000 00:18 458639 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/ctabix.so 7f93fd812000-7f93fd814000 rw-p 00000000 00:00 0 7f93fd814000-7f93fd83b000 r-xp 00000000 fe:00 949810 /usr/lib/python2.7/lib-dynload/_ctypes.so 7f93fd83b000-7f93fda3a000 ---p 00027000 fe:00 949810 /usr/lib/python2.7/lib-dynload/_ctypes.so 7f93fda3a000-7f93fda3b000 r--p 00026000 fe:00 949810 /usr/lib/python2.7/lib-dynload/_ctypes.so 7f93fda3b000-7f93fda3f000 rw-p 00027000 fe:00 949810 /usr/lib/python2.7/lib-dynload/_ctypes.so 7f93fda3f000-7f93fda40000 rw-p 00000000 00:00 0 7f93fda40000-7f93fdb10000 r-xp 00000000 00:18 458638 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so 7f93fdb10000-7f93fdc10000 ---p 000d0000 00:18 458638 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so 7f93fdc10000-7f93fdc20000 rw-p 000d0000 00:18 458638 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so 7f93fdc20000-7f93fdc25000 rw-p 00000000 00:00 0 7f93fdc25000-7f93fdc44000 r-xp 00000000 fe:00 949804 /usr/lib/python2.7/lib-dynload/_io.so 7f93fdc44000-7f93fde44000 ---p 0001f000 fe:00 949804 /usr/lib/python2.7/lib-dynload/_io.so 7f93fde44000-7f93fde45000 r--p 0001f000 fe:00 949804 /usr/lib/python2.7/lib-dynload/_io.so 7f93fde45000-7f93fde4e000 rw-p 00020000 fe:00 949804 /usr/lib/python2.7/lib-dynload/_io.so 7f93fde4e000-7f93fdf0f000 rw-p 00000000 00:00 0 7f93fdf0f000-7f93fdf12000 r-xp 00000000 fe:00 949801 /usr/lib/python2.7/lib-dynload/_heapq.so 7f93fdf12000-7f93fe111000 ---p 00003000 fe:00 949801 /usr/lib/python2.7/lib-dynload/_heapq.so 7f93fe111000-7f93fe112000 r--p 00002000 fe:00 949801 /usr/lib/python2.7/lib-dynload/_heapq.so 7f93fe112000-7f93fe114000 rw-p 00003000 fe:00 949801 /usr/lib/python2.7/lib-dynload/_heapq.so 7f93fe114000-7f93fe196000 rw-p 00000000 00:00 0 7f93fe196000-7f93fe1ab000 r-xp 00000000 fe:00 122656 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f93fe1ab000-7f93fe3ab000 ---p 00015000 fe:00 122656 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f93fe3ab000-7f93fe3ac000 rw-p 00015000 fe:00 122656 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f93fe3ac000-7f93fe529000 r-xp 00000000 fe:00 131366 /lib/x86_64-linux-gnu/libc-2.13.so 7f93fe529000-7f93fe729000 ---p 0017d000 fe:00 131366 /lib/x86_64-linux-gnu/libc-2.13.so 7f93fe729000-7f93fe72d000 r--p 0017d000 fe:00 131366 /lib/x86_64-linux-gnu/libc-2.13.so 7f93fe72d000-7f93fe72e000 rw-p 00181000 fe:00 131366 /lib/x86_64-linux-gnu/libc-2.13.so 7f93fe72e000-7f93fe733000 rw-p 00000000 00:00 0 7f93fe733000-7f93fe7b4000 r-xp 00000000 fe:00 131404 /lib/x86_64-linux-gnu/libm-2.13.so 7f93fe7b4000-7f93fe9b3000 ---p 00081000 fe:00 131404 /lib/x86_64-linux-gnu/libm-2.13.so 7f93fe9b3000-7f93fe9b4000 r--p 00080000 fe:00 131404 /lib/x86_64-linux-gnu/libm-2.13.so 7f93fe9b4000-7f93fe9b5000 rw-p 00081000 fe:00 131404 /lib/x86_64-linux-gnu/libm-2.13.so 7f93fe9b5000-7f93fe9cb000 r-xp 00000000 fe:00 909634 /usr/lib/x86_64-linux-gnu/libz.so.1.2.6 7f93fe9cb000-7f93febca000 ---p 00016000 fe:00 909634 /usr/lib/x86_64-linux-gnu/libz.so.1.2.6 7f93febca000-7f93febcb000 rw-p 00015000 fe:00 909634 /usr/lib/x86_64-linux-gnu/libz.so.1.2.6 7f93febcb000-7f93fed68000 r-xp 00000000 fe:00 909753 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0 7f93fed68000-7f93fef67000 ---p 0019d000 fe:00 909753 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0 7f93fef67000-7f93fef8d000 rw-p 0019c000 fe:00 909753 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0 7f93fef8d000-7f93fef91000 rw-p 00000000 00:00 0 7f93fef91000-7f93fefdc000 r-xp 00000000 fe:00 909754 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0 7f93fefdc000-7f93ff1db000 ---p 0004b000 fe:00 909754 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0 7f93ff1db000-7f93ff1e3000 rw-p 0004a000 fe:00 909754 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0 7f93ff1e3000-7f93ff1e5000 r-xp 00000000 fe:00 131419 /lib/x86_64-linux-gnu/libutil-2.13.so 7f93ff1e5000-7f93ff3e4000 ---p 00002000 fe:00 131419 /lib/x86_64-linux-gnu/libutil-2.13.so 7f93ff3e4000-7f93ff3e5000 r--p 00001000 fe:00 131419 /lib/x86_64-linux-gnu/libutil-2.13.so 7f93ff3e5000-7f93ff3e6000 rw-p 00002000 fe:00 131419 /lib/x86_64-linux-gnu/libutil-2.13.so 7f93ff3e6000-7f93ff3e8000 r-xp 00000000 fe:00 131412 /lib/x86_64-linux-gnu/libdl-2.13.so 7f93ff3e8000-7f93ff5e8000 ---p 00002000 fe:00 131412 /lib/x86_64-linux-gnu/libdl-2.13.so 7f93ff5e8000-7f93ff5e9000 r--p 00002000 fe:00 131412 /lib/x86_64-linux-gnu/libdl-2.13.so 7f93ff5e9000-7f93ff5ea000 rw-p 00003000 fe:00 131412 /lib/x86_64-linux-gnu/libdl-2.13.so 7f93ff5ea000-7f93ff601000 r-xp 00000000 fe:00 131416 /lib/x86_64-linux-gnu/libpthread-2.13.so 7f93ff601000-7f93ff800000 ---p 00017000 fe:00 131416 /lib/x86_64-linux-gnu/libpthread-2.13.so 7f93ff800000-7f93ff801000 r--p 00016000 fe:00 131416 /lib/x86_64-linux-gnu/libpthread-2.13.so 7f93ff801000-7f93ff802000 rw-p 00017000 fe:00 131416 /lib/x86_64-linux-gnu/libpthread-2.13.so 7f93ff802000-7f93ff806000 rw-p 00000000 00:00 0 7f93ff806000-7f93ff825000 r-xp 00000000 fe:00 131420 /lib/x86_64-linux-gnu/ld-2.13.so 7f93ff859000-7f93ff95d000 rw-p 00000000 00:00 0 7f93ff98f000-7f93ffa17000 rw-p 00000000 00:00 0 7f93ffa21000-7f93ffa22000 rw-p 00000000 00:00 0 7f93ffa22000-7f93ffa23000 rwxp 00000000 00:00 0 7f93ffa23000-7f93ffa25000 rw-p 00000000 00:00 0 7f93ffa25000-7f93ffa26000 r--p 0001f000 fe:00 131420 /lib/x86_64-linux-gnu/ld-2.13.so 7f93ffa26000-7f93ffa27000 rw-p 00020000 fe:00 131420 /lib/x86_64-linux-gnu/ld-2.13.so 7f93ffa27000-7f93ffa28000 rw-p 00000000 00:00 0 7fff744fb000-7fff7451c000 rw-p 00000000 00:00 0 [stack] 7fff74589000-7fff7458a000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public 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Jeremy Goecks