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jeromekelleher/gist:074ac7f7e0f0c95a7be4

Created August 13, 2015 11:44
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Stacktrace of htslib error.
Raw
gistfile1.txt
(gdb) run scripts/download_data.py
Starting program: /usr/bin/python scripts/download_data.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Cleaning out directory '/home/jk/work/github/server/ga4gh-downloaded-data/dataset1/reads/low-coverage'
Downloading index for 'ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam'
[M::test_and_fetch] downloading file 'ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.bai' to local directory
Writing 'HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam'
*** buffer overflow detected ***: /usr/bin/python terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x731ff)[0x7ffff6f661ff]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7ffff6fe94c7]
/lib/x86_64-linux-gnu/libc.so.6(+0xf46e0)[0x7ffff6fe76e0]
/lib/x86_64-linux-gnu/libc.so.6(+0xf6437)[0x7ffff6fe9437]
/home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so(+0xae1ae)[0x7ffff530c1ae]
/home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so(+0xae3ca)[0x7ffff530c3ca]
/home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so(knet_read+0xd0)[0x7ffff530d050]
/home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so(+0xaf404)[0x7ffff530d404]
/home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so(hread2+0x98)[0x7ffff530d8f8]
/home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so(bgzf_read_block+0x3cd)[0x7ffff530a45d]
/home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so(bgzf_read+0x7c)[0x7ffff530b1ac]
/home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so(bam_read1+0x2d)[0x7ffff530f07d]
/home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so(+0xb126c)[0x7ffff530f26c]
/home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so(hts_itr_next+0xdf)[0x7ffff52f029f]
/home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so(+0x196c0)[0x7ffff52776c0]
/home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so(+0x4a7e3)[0x7ffff52a87e3]
/usr/bin/python(PyEval_EvalFrameEx+0x72e)[0x4ca1de]
/usr/bin/python(PyEval_EvalCodeEx+0x411)[0x4c87a1]
/usr/bin/python(PyEval_EvalFrameEx+0x1e11)[0x4cb8c1]
/usr/bin/python[0x4e5fe8]
/usr/bin/python(PyEval_EvalFrameEx+0x28bb)[0x4cc36b]
/usr/bin/python(PyEval_EvalCodeEx+0x411)[0x4c87a1]
/usr/bin/python(PyEval_EvalFrameEx+0x1e11)[0x4cb8c1]
/usr/bin/python(PyEval_EvalCodeEx+0x411)[0x4c87a1]
/usr/bin/python[0x5030ef]
/usr/bin/python(PyRun_FileExFlags+0x82)[0x4f8c72]
/usr/bin/python(PyRun_SimpleFileExFlags+0x197)[0x4f7d77]
/usr/bin/python(Py_Main+0x562)[0x4982f2]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7ffff6f14b45]
/usr/bin/python[0x497ca0]
======= Memory map: ========
00400000-0071f000 r-xp 00000000 09:00 525847 /usr/bin/python2.7
0091e000-0091f000 r--p 0031e000 09:00 525847 /usr/bin/python2.7
0091f000-0099c000 rw-p 0031f000 09:00 525847 /usr/bin/python2.7
0099c000-0262d000 rw-p 00000000 00:00 0 [heap]
7ffff2855000-7ffff286b000 r-xp 00000000 09:00 784949 /lib/x86_64-linux-gnu/libgcc_s.so.1
7ffff286b000-7ffff2a6a000 ---p 00016000 09:00 784949 /lib/x86_64-linux-gnu/libgcc_s.so.1
7ffff2a6a000-7ffff2a6b000 rw-p 00015000 09:00 784949 /lib/x86_64-linux-gnu/libgcc_s.so.1
7ffff2a6b000-7ffff2a7f000 r-xp 00000000 09:00 788783 /lib/x86_64-linux-gnu/libresolv-2.19.so
7ffff2a7f000-7ffff2c7e000 ---p 00014000 09:00 788783 /lib/x86_64-linux-gnu/libresolv-2.19.so
7ffff2c7e000-7ffff2c7f000 r--p 00013000 09:00 788783 /lib/x86_64-linux-gnu/libresolv-2.19.so
7ffff2c7f000-7ffff2c80000 rw-p 00014000 09:00 788783 /lib/x86_64-linux-gnu/libresolv-2.19.so
7ffff2c80000-7ffff2c82000 rw-p 00000000 00:00 0
7ffff2c82000-7ffff2c87000 r-xp 00000000 09:00 788787 /lib/x86_64-linux-gnu/libnss_dns-2.19.so
7ffff2c87000-7ffff2e86000 ---p 00005000 09:00 788787 /lib/x86_64-linux-gnu/libnss_dns-2.19.so
7ffff2e86000-7ffff2e87000 r--p 00004000 09:00 788787 /lib/x86_64-linux-gnu/libnss_dns-2.19.so
7ffff2e87000-7ffff2e88000 rw-p 00005000 09:00 788787 /lib/x86_64-linux-gnu/libnss_dns-2.19.so
7ffff2e88000-7ffff2e93000 r-xp 00000000 09:00 788779 /lib/x86_64-linux-gnu/libnss_files-2.19.so
7ffff2e93000-7ffff3092000 ---p 0000b000 09:00 788779 /lib/x86_64-linux-gnu/libnss_files-2.19.so
7ffff3092000-7ffff3093000 r--p 0000a000 09:00 788779 /lib/x86_64-linux-gnu/libnss_files-2.19.so
7ffff3093000-7ffff3094000 rw-p 0000b000 09:00 788779 /lib/x86_64-linux-gnu/libnss_files-2.19.so
7ffff3094000-7ffff3194000 rw-p 00000000 00:00 0
7ffff3194000-7ffff319e000 r-xp 00000000 09:00 922461 /usr/lib/python2.7/dist-packages/simplejson/_speedups.x86_64-linux-gnu.so
7ffff319e000-7ffff339d000 ---p 0000a000 09:00 922461 /usr/lib/python2.7/dist-packages/simplejson/_speedups.x86_64-linux-gnu.so
7ffff339d000-7ffff339e000 r--p 00009000 09:00 922461 /usr/lib/python2.7/dist-packages/simplejson/_speedups.x86_64-linux-gnu.so
7ffff339e000-7ffff339f000 rw-p 0000a000 09:00 922461 /usr/lib/python2.7/dist-packages/simplejson/_speedups.x86_64-linux-gnu.so
7ffff339f000-7ffff345f000 rw-p 00000000 00:00 0
7ffff345f000-7ffff34ff000 r-xp 00000000 fd:00 25770016777 /home/jk/.local/lib/python2.7/site-packages/cryptography/_Cryptography_cffi_a269d620xd5c405b7.so
7ffff34ff000-7ffff36fe000 ---p 000a0000 fd:00 25770016777 /home/jk/.local/lib/python2.7/site-packages/cryptography/_Cryptography_cffi_a269d620xd5c405b7.so
7ffff36fe000-7ffff36ff000 r--p 0009f000 fd:00 25770016777 /home/jk/.local/lib/python2.7/site-packages/cryptography/_Cryptography_cffi_a269d620xd5c405b7.so
7ffff36ff000-7ffff370b000 rw-p 000a0000 fd:00 25770016777 /home/jk/.local/lib/python2.7/site-packages/cryptography/_Cryptography_cffi_a269d620xd5c405b7.so
7ffff370b000-7ffff3d0b000 rw-p 00000000 00:00 0
7ffff3d0b000-7ffff3d28000 r-xp 00000000 fd:00 45097201665 /home/jk/.local/lib/python2.7/site-packages/_cffi_backend.so
7ffff3d28000-7ffff3f28000 ---p 0001d000 fd:00 45097201665 /home/jk/.local/lib/python2.7/site-packages/_cffi_backend.so
7ffff3f28000-7ffff3f29000 r--p 0001d000 fd:00 45097201665 /home/jk/.local/lib/python2.7/site-packages/_cffi_backend.so
7ffff3f29000-7ffff3f2e000 rw-p 0001e000 fd:00 45097201665 /home/jk/.local/lib/python2.7/site-packages/_cffi_backend.so
7ffff3f2e000-7ffff4130000 rw-p 00000000 00:00 0
7ffff4130000-7ffff4134000 r-xp 00000000 09:00 784944 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7ffff4134000-7ffff4333000 ---p 00004000 09:00 784944 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7ffff4333000-7ffff4334000 r--p 00003000 09:00 784944 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7ffff4334000-7ffff4335000 rw-p 00004000 09:00 784944 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7ffff4335000-7ffff43f5000 rw-p 00000000 00:00 0
7ffff43f5000-7ffff4409000 r-xp 00000000 09:00 785744 /usr/lib/python2.7/lib-dynload/_ssl.x86_64-linux-gnu.so
7ffff4409000-7ffff4608000 ---p 00014000 09:00 785744 /usr/lib/python2.7/lib-dynload/_ssl.x86_64-linux-gnu.so
7ffff4608000-7ffff4609000 r--p 00013000 09:00 785744 /usr/lib/python2.7/lib-dynload/_ssl.x86_64-linux-gnu.so
7ffff4609000-7ffff460d000 rw-p 00014000 09:00 785744 /usr/lib/python2.7/lib-dynload/_ssl.x86_64-linux-gnu.so
7ffff460d000-7ffff470d000 rw-p 00000000 00:00 0
7ffff470d000-7ffff47f8000 r-xp 00000000 fd:00 6445662215 /home/jk/.local/lib/python2.7/site-packages/pysam/csamtools.so
7ffff47f8000-7ffff49f8000 ---p 000eb000 fd:00 6445662215 /home/jk/.local/lib/python2.7/site-packages/pysam/csamtools.so
7ffff49f8000-7ffff49f9000 r--p 000eb000 fd:00 6445662215 /home/jk/.local/lib/python2.7/site-packages/pysam/csamtools.so
7ffff49f9000-7ffff49fc000 rw-p 000ec000 fd:00 6445662215 /home/jk/.local/lib/python2.7/site-packages/pysam/csamtools.so
7ffff49fc000-7ffff49fd000 rw-p 00000000 00:00 0
7ffff49fd000-7ffff4ade000 r-xp 00000000 fd:00 6445662208 /home/jk/.local/lib/python2.7/site-packages/pysam/cbcf.so
7ffff4ade000-7ffff4cdd000 ---p 000e1000 fd:00 6445662208 /home/jk/.local/lib/python2.7/site-packages/pysam/cbcf.so
7ffff4cdd000-7ffff4cdf000 r--p 000e0000 fd:00 6445662208 /home/jk/.local/lib/python2.7/site-packages/pysam/cbcf.so
7ffff4cdf000-7ffff4cef000 rw-p 000e2000 fd:00 6445662208 /home/jk/.local/lib/python2.7/site-packages/pysam/cbcf.so
7ffff4cef000-7ffff4cf1000 rw-p 00000000 00:00 0
7ffff4cf1000-7ffff4d78000 r-xp 00000000 fd:00 6445662209 /home/jk/.local/lib/python2.7/site-packages/pysam/cvcf.so
7ffff4d78000-7ffff4f77000 ---p 00087000 fd:00 6445662209 /home/jk/.local/lib/python2.7/site-packages/pysam/cvcf.so
7ffff4f77000-7ffff4f78000 r--p 00086000 fd:00 6445662209 /home/jk/.local/lib/python2.7/site-packages/pysam/cvcf.so
7ffff4f78000-7ffff4f81000 rw-p 00087000 fd:00 6445662209 /home/jk/.local/lib/python2.7/site-packages/pysam/cvcf.so
7ffff4f81000-7ffff4f83000 rw-p 00000000 00:00 0
7ffff4f83000-7ffff501a000 r-xp 00000000 fd:00 6442659903 /home/jk/.local/lib/python2.7/site-packages/pysam/cfaidx.so
7ffff501a000-7ffff5219000 ---p 00097000 fd:00 6442659903 /home/jk/.local/lib/python2.7/site-packages/pysam/cfaidx.so
7ffff5219000-7ffff521a000 r--p 00096000 fd:00 6442659903 /home/jk/.local/lib/python2.7/site-packages/pysam/cfaidx.so
7ffff521a000-7ffff521e000 rw-p 00097000 fd:00 6442659903 /home/jk/.local/lib/python2.7/site-packages/pysam/cfaidx.so
7ffff521e000-7ffff525e000 rw-p 00000000 00:00 0
7ffff525e000-7ffff5367000 r-xp 00000000 fd:00 6445662212 /home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so
7ffff5367000-7ffff5566000 ---p 00109000 fd:00 6445662212 /home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so
7ffff5566000-7ffff5567000 r--p 00108000 fd:00 6445662212 /home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so
7ffff5567000-7ffff5577000 rw-p 00109000 fd:00 6445662212 /home/jk/.local/lib/python2.7/site-packages/pysam/calignmentfile.so
7ffff5577000-7ffff557a000 rw-p 00000000 00:00 0
7ffff557a000-7ffff5601000 r-xp 00000000 fd:00 6445662213 /home/jk/.local/lib/python2.7/site-packages/pysam/csamfile.so
7ffff5601000-7ffff5800000 ---p 00087000 fd:00 6445662213 /home/jk/.local/lib/python2.7/site-packages/pysam/csamfile.so
7ffff5800000-7ffff5801000 r--p 00086000 fd:00 6445662213 /home/jk/.local/lib/python2.7/site-packages/pysam/csamfile.so
7ffff5801000-7ffff5802000 rw-p 00087000 fd:00 6445662213 /home/jk/.local/lib/python2.7/site-packages/pysam/csamfile.so
7ffff5802000-7ffff5803000 rw-p 00000000 00:00 0
7ffff5803000-7ffff5823000 r-xp 00000000 fd:00 6445662210 /home/jk/.local/lib/python2.7/site-packages/pysam/TabProxies.so
7ffff5823000-7ffff5a22000 ---p 00020000 fd:00 6445662210 /home/jk/.local/lib/python2.7/site-packages/pysam/TabProxies.so
7ffff5a22000-7ffff5a23000 r--p 0001f000 fd:00 6445662210 /home/jk/.local/lib/python2.7/site-packages/pysam/TabProxies.so
7ffff5a23000-7ffff5a26000 rw-p 00020000 fd:00 6445662210 /home/jk/.local/lib/python2.7/site-packages/pysam/TabProxies.so
7ffff5a26000-7ffff5a27000 rw-p 00000000 00:00 0
7ffff5a27000-7ffff5acb000 r-xp 00000000 fd:00 6445662211 /home/jk/.local/lib/python2.7/site-packages/pysam/ctabix.so
7ffff5acb000-7ffff5ccb000 ---p 000a4000 fd:00 6445662211 /home/jk/.local/lib/python2.7/site-packages/pysam/ctabix.so
7ffff5ccb000-7ffff5ccd000 r--p 000a4000 fd:00 6445662211 /home/jk/.local/lib/python2.7/site-packages/pysam/ctabix.so
7ffff5ccd000-7ffff5cd4000 rw-p 000a6000 fd:00 6445662211 /home/jk/.local/lib/python2.7/site-packages/pysam/ctabix.so
7ffff5cd4000-7ffff5cdb000 r-xp 00000000 09:00 525825 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.2
7ffff5cdb000-7ffff5eda000 ---p 00007000 09:00 525825 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.2
7ffff5eda000-7ffff5edb000 r--p 00006000 09:00 525825 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.2
7ffff5edb000-7ffff5edc000 rw-p 00007000 09:00 525825 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.2
7ffff5edc000-7ffff5efa000 r-xp 00000000 09:00 785786 /usr/lib/python2.7/lib-dynload/_ctypes.x86_64-linux-gnu.so
7ffff5efa000-7ffff60f9000 ---p 0001e000 09:00 785786 /usr/lib/python2.7/lib-dynload/_ctypes.x86_64-linux-gnu.so
7ffff60f9000-7ffff60fa000 r--p 0001d000 09:00 785786 /usr/lib/python2.7/lib-dynload/_ctypes.x86_64-linux-gnu.so
7ffff60fa000-7ffff60fe000 rw-p 0001e000 09:00 785786 /usr/lib/python2.7/lib-dynload/_ctypes.x86_64-linux-gnu.so
7ffff60fe000-7ffff613f000 rw-p 00000000 00:00 0
7ffff613f000-7ffff630a000 r-xp 00000000 09:00 524030 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7ffff630a000-7ffff650a000 ---p 001cb000 09:00 524030 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7ffff650a000-7ffff6527000 r--p 001cb000 09:00 524030 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7ffff6527000-7ffff6537000 rw-p 001e8000 09:00 524030 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7ffff6537000-7ffff653a000 rw-p 00000000 00:00 0
7ffff653a000-7ffff6590000 r-xp 00000000 09:00 539041 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7ffff6590000-7ffff6790000 ---p 00056000 09:00 539041 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7ffff6790000-7ffff6793000 r--p 00056000 09:00 539041 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7ffff6793000-7ffff679a000 rw-p 00059000 09:00 539041 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7ffff679a000-7ffff67a0000 r-xp 00000000 09:00 785757 /usr/lib/python2.7/lib-dynload/_hashlib.x86_64-linux-gnu.so
7ffff67a0000-7ffff699f000 ---p 00006000 09:00 785757 /usr/lib/python2.7/lib-dynload/_hashlib.x86_64-linux-gnu.so
7ffff699f000-7ffff69a0000 r--p 00005000 09:00 785757 /usr/lib/python2.7/lib-dynload/_hashlib.x86_64-linux-gnu.so
7ffff69a0000-7ffff69a1000 rw-p 00006000 09:00 785757 /usr/lib/python2.7/lib-dynload/_hashlib.x86_64-linux-gnu.so
7ffff69a1000-7ffff6a62000 rw-p 00000000 00:00 0
7ffff6a62000-7ffff6ae6000 r-xp 00000000 fd:00 6445662214 /home/jk/.local/lib/python2.7/site-packages/pysam/libchtslib.so
7ffff6ae6000-7ffff6ce6000 ---p 00084000 fd:00 6445662214 /home/jk/.local/lib/python2.7/site-packages/pysam/libchtslib.so
7ffff6ce6000-7ffff6ce7000 r--p 00084000 fd:00 6445662214 /home/jk/.local/lib/python2.7/site-packages/pysam/libchtslib.so
7ffff6ce7000-7ffff6ce8000 rw-p 00085000 fd:00 6445662214 /home/jk/.local/lib/python2.7/site-packages/pysam/libchtslib.so
7ffff6ce8000-7ffff6d68000 rw-p 00000000 00:00 0
7ffff6d68000-7ffff6ef3000 r--p 00000000 09:00 526831 /usr/lib/locale/locale-archive
7ffff6ef3000-7ffff7092000 r-xp 00000000 09:00 788795 /lib/x86_64-linux-gnu/libc-2.19.so
7ffff7092000-7ffff7292000 ---p 0019f000 09:00 788795 /lib/x86_64-linux-gnu/libc-2.19.so
7ffff7292000-7ffff7296000 r--p 0019f000 09:00 788795 /lib/x86_64-linux-gnu/libc-2.19.so
7ffff7296000-7ffff7298000 rw-p 001a3000 09:00 788795 /lib/x86_64-linux-gnu/libc-2.19.so
7ffff7298000-7ffff729c000 rw-p 00000000 00:00 0
7ffff729c000-7ffff739c000 r-xp 00000000 09:00 788794 /lib/x86_64-linux-gnu/libm-2.19.so
7ffff739c000-7ffff759b000 ---p 00100000 09:00 788794 /lib/x86_64-linux-gnu/libm-2.19.so
7ffff759b000-7ffff759c000 r--p 000ff000 09:00 788794 /lib/x86_64-linux-gnu/libm-2.19.so
7ffff759c000-7ffff759d000 rw-p 00100000 09:00 788794 /lib/x86_64-linux-gnu/libm-2.19.so
7ffff759d000-7ffff75b7000 r-xp 00000000 09:00 785211 /lib/x86_64-linux-gnu/libz.so.1.2.8
7ffff75b7000-7ffff77b6000 ---p 0001a000 09:00 785211 /lib/x86_64-linux-gnu/libz.so.1.2.8
7ffff77b6000-7ffff77b7000 r--p 00019000 09:00 785211 /lib/x86_64-linux-gnu/libz.so.1.2.8
7ffff77b7000-7ffff77b8000 rw-p 0001a000 09:00 785211 /lib/x86_64-linux-gnu/libz.so.1.2.8
7ffff77b8000-7ffff77ba000 r-xp 00000000 09:00 788777 /lib/x86_64-linux-gnu/libutil-2.19.so
7ffff77ba000-7ffff79b9000 ---p 00002000 09:00 788777 /lib/x86_64-linux-gnu/libutil-2.19.so
7ffff79b9000-7ffff79ba000 r--p 00001000 09:00 788777 /lib/x86_64-linux-gnu/libutil-2.19.so
7ffff79ba000-7ffff79bb000 rw-p 00002000 09:00 788777 /lib/x86_64-linux-gnu/libutil-2.19.so
7ffff79bb000-7ffff79be000 r-xp 00000000 09:00 788775 /lib/x86_64-linux-gnu/libdl-2.19.so
7ffff79be000-7ffff7bbd000 ---p 00003000 09:00 788775 /lib/x86_64-linux-gnu/libdl-2.19.so
7ffff7bbd000-7ffff7bbe000 r--p 00002000 09:00 788775 /lib/x86_64-linux-gnu/libdl-2.19.so
7ffff7bbe000-7ffff7bbf000 rw-p 00003000 09:00 788775 /lib/x86_64-linux-gnu/libdl-2.19.so
7ffff7bbf000-7ffff7bd7000 r-xp 00000000 09:00 788788 /lib/x86_64-linux-gnu/libpthread-2.19.so
7ffff7bd7000-7ffff7dd6000 ---p 00018000 09:00 788788 /lib/x86_64-linux-gnu/libpthread-2.19.so
7ffff7dd6000-7ffff7dd7000 r--p 00017000 09:00 788788 /lib/x86_64-linux-gnu/libpthread-2.19.so
7ffff7dd7000-7ffff7dd8000 rw-p 00018000 09:00 788788 /lib/x86_64-linux-gnu/libpthread-2.19.so
7ffff7dd8000-7ffff7ddc000 rw-p 00000000 00:00 0
7ffff7ddc000-7ffff7dfc000 r-xp 00000000 09:00 788771 /lib/x86_64-linux-gnu/ld-2.19.so
7ffff7e27000-7ffff7ee7000 rw-p 00000000 00:00 0
7ffff7f18000-7ffff7fdd000 rw-p 00000000 00:00 0
7ffff7ff3000-7ffff7ff5000 rw-p 00000000 00:00 0
7ffff7ff5000-7ffff7ff6000 rwxp 00000000 00:00 0
7ffff7ff6000-7ffff7ff8000 rw-p 00000000 00:00 0
7ffff7ff8000-7ffff7ffa000 r-xp 00000000 00:00 0 [vdso]
7ffff7ffa000-7ffff7ffc000 r--p 00000000 00:00 0 [vvar]
7ffff7ffc000-7ffff7ffd000 r--p 00020000 09:00 788771 /lib/x86_64-linux-gnu/ld-2.19.so
7ffff7ffd000-7ffff7ffe000 rw-p 00021000 09:00 788771 /lib/x86_64-linux-gnu/ld-2.19.so
7ffff7ffe000-7ffff7fff000 rw-p 00000000 00:00 0
7ffffffde000-7ffffffff000 rw-p 00000000 00:00 0 [stack]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Program received signal SIGABRT, Aborted.
0x00007ffff6f28107 in __GI_raise (sig=sig@entry=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:56
56 ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) bt
#0 0x00007ffff6f28107 in __GI_raise (sig=sig@entry=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:56
#1 0x00007ffff6f294e8 in __GI_abort () at abort.c:89
#2 0x00007ffff6f66204 in __libc_message (do_abort=do_abort@entry=2,
fmt=fmt@entry=0x7ffff7056a2b "*** %s ***: %s terminated\n") at ../sysdeps/posix/libc_fatal.c:175
#3 0x00007ffff6fe94c7 in __GI___fortify_fail (msg=msg@entry=0x7ffff70569c2 "buffer overflow detected")
at fortify_fail.c:31
#4 0x00007ffff6fe76e0 in __GI___chk_fail () at chk_fail.c:28
#5 0x00007ffff6fe9437 in __fdelt_chk (d=d@entry=-1) at fdelt_chk.c:25
#6 0x00007ffff530c1ae in socket_wait (fd=fd@entry=-1, is_read=is_read@entry=1) at htslib/knetfile.c:67
#7 0x00007ffff530c3ca in my_netread (fd=-1, buf=buf@entry=0x107f600, len=len@entry=32768)
at htslib/knetfile.c:188
#8 0x00007ffff530d050 in knet_read (fp=0x1071a00, buf=0x107f600, len=32768) at htslib/knetfile.c:538
#9 0x00007ffff530d404 in refill_buffer (fp=fp@entry=0xb08250) at htslib/hfile.c:120
#10 0x00007ffff530d8f8 in hread2 (fp=0xb08250, destv=<optimized out>, nbytes=18, nread=0)
at htslib/hfile.c:170
#11 0x00007ffff530a45d in hread (nbytes=18, buffer=0x7fffffffd840, fp=0xb08250)
at htslib/htslib/hfile.h:155
#12 bgzf_read_block (fp=fp@entry=0xb486b0) at htslib/bgzf.c:455
#13 0x00007ffff530b1ac in bgzf_read (fp=0xb486b0, data=<optimized out>, length=4) at htslib/bgzf.c:557
#14 0x00007ffff530f07d in bam_read1 (fp=0xb486b0, b=b@entry=0x102b600) at htslib/sam.c:329
#15 0x00007ffff530f26c in bam_readrec (fp=<optimized out>, ignored=<optimized out>, bv=0x102b600,
tid=0x7fffffffd98c, beg=0x7fffffffd990, end=0x7fffffffd994) at htslib/sam.c:462
#16 0x00007ffff52f029f in hts_itr_next (fp=0xb486b0, iter=0x2588ed0, r=0x102b600, data=0x101b790)
at htslib/hts.c:1565
#17 0x00007ffff52776c0 in __pyx_f_5pysam_14calignmentfile_17IteratorRowRegion_cnext (
__pyx_v_self=0x7ffff5259050) at pysam/calignmentfile.c:18820
#18 0x00007ffff52a87e3 in __pyx_pf_5pysam_14calignmentfile_17IteratorRowRegion_4__next__ (
__pyx_v_self=0x7ffff5259050) at pysam/calignmentfile.c:18881
#19 __pyx_pw_5pysam_14calignmentfile_17IteratorRowRegion_5__next__ (
__pyx_v_self=<pysam.calignmentfile.IteratorRowRegion at remote 0x7ffff5259050>)
at pysam/calignmentfile.c:18855
#20 0x00000000004ca1de in PyEval_EvalFrameEx () at ../Python/ceval.c:2510
#21 0x00000000004c87a1 in PyEval_EvalCodeEx () at ../Python/ceval.c:3265
#22 0x00000000004cb8c1 in fast_function (nk=<optimized out>, na=<optimized out>, n=<optimized out>,
pp_stack=<optimized out>, func=<optimized out>) at ../Python/ceval.c:4129
#23 call_function (oparg=<optimized out>, pp_stack=<optimized out>) at ../Python/ceval.c:4054
#24 PyEval_EvalFrameEx () at ../Python/ceval.c:2679
#25 0x00000000004e5fe8 in PyEval_EvalCodeEx (closure=<optimized out>, defcount=<optimized out>,
defs=<optimized out>, kwcount=<optimized out>, kws=<optimized out>, argcount=<optimized out>,
args=<optimized out>, locals=<optimized out>, globals=<optimized out>, co=<optimized out>)
at ../Python/ceval.c:3265
#26 function_call.lto_priv () at ../Objects/funcobject.c:526
#27 0x00000000004cc36b in PyObject_Call (kw=<optimized out>, arg=<optimized out>, func=<optimized out>)
at ../Objects/abstract.c:2529
#28 ext_do_call (nk=<optimized out>, na=<optimized out>, flags=<optimized out>,
pp_stack=<optimized out>, func=<optimized out>) at ../Python/ceval.c:4346
#29 PyEval_EvalFrameEx () at ../Python/ceval.c:2718
#30 0x00000000004c87a1 in PyEval_EvalCodeEx () at ../Python/ceval.c:3265
#31 0x00000000004cb8c1 in fast_function (nk=<optimized out>, na=<optimized out>, n=<optimized out>,
pp_stack=<optimized out>, func=<optimized out>) at ../Python/ceval.c:4129
#32 call_function (oparg=<optimized out>, pp_stack=<optimized out>) at ../Python/ceval.c:4054
#33 PyEval_EvalFrameEx () at ../Python/ceval.c:2679
#34 0x00000000004c87a1 in PyEval_EvalCodeEx () at ../Python/ceval.c:3265
#35 0x00000000005030ef in PyEval_EvalCode (
locals={'pysam': <module at remote 0x7ffff6cebde0>, 'parseArgs': <function at remote 0x7ffff309d410>, 'unicode_literals': <_Feature(mandatory=(3, 0, 0, 'alpha', 0), optional=(2, 6, 0, 'alpha', 2), compiler_flag=131072) at remote 0x7ffff7ea4c68>, 'utils': <module at remote 0x7ffff46dd7c0>, 'sources': {u'ebi': <type at remote 0x1053650>, u'ncbi': <type at remote 0xc45dc0>}, 'NcbiFileDownloader': <type at remote 0xc45dc0>, '__package__': None, 'EbiFileDownloader': <type at remote 0x1053650>, 'main': <function at remote 0x7ffff309daa0>, 'glob': <module at remote 0x7ffff6d31718>, 'cleanDir': <function at remote 0x7ffff309d3---Type <return> to continue, or q <return> to quit---
98>, 'division': <_Feature(mandatory=(3, 0, 0, 'alpha', 0), optional=(2, 2, 0, 'alpha', 2), compiler_flag=8192) at remote 0x7ffff7ea4b48>, '__builtins__': <module at remote 0x7ffff7f98b08>, '__file__': 'scripts/download_data.py', 'args': <Namespace(num_vcf_records=5, source=u'ncbi', num_retries=3, samples=u'HG00096,HG00533,HG00534', dir_name=u'ga4gh-downloaded-data') at remote 0x7ffff30a1dd0>, 'mkdirAn...(truncated),
globals={'pysam': <module at remote 0x7ffff6cebde0>, 'parseArgs': <function at remote 0x7ffff309d410>, 'unicode_literals': <_Feature(mandatory=(3, 0, 0, 'alpha', 0), optional=(2, 6, 0, 'alpha', 2), compiler_flag=131072) at remote 0x7ffff7ea4c68>, 'utils': <module at remote 0x7ffff46dd7c0>, 'sources': {u'ebi': <type at remote 0x1053650>, u'ncbi': <type at remote 0xc45dc0>}, 'NcbiFileDownloader': <type at remote 0xc45dc0>, '__package__': None, 'EbiFileDownloader': <type at remote 0x1053650>, 'main': <function at remote 0x7ffff309daa0>, 'glob': <module at remote 0x7ffff6d31718>, 'cleanDir': <function at remote 0x7ffff309d398>, 'division': <_Feature(mandatory=(3, 0, 0, 'alpha', 0), optional=(2, 2, 0, 'alpha', 2), compiler_flag=8192) at remote 0x7ffff7ea4b48>, '__builtins__': <module at remote 0x7ffff7f98b08>, '__file__': 'scripts/download_data.py', 'args': <Namespace(num_vcf_records=5, source=u'ncbi', num_retries=3, samples=u'HG00096,HG00533,HG00534', dir_name=u'ga4gh-downloaded-data') at remote 0x7ffff30a1dd0>, 'mkdirAn...(truncated),
co=0x7ffff6d2a5b0) at ../Python/ceval.c:667
#36 run_mod.lto_priv () at ../Python/pythonrun.c:1371
#37 0x00000000004f8c72 in PyRun_FileExFlags () at ../Python/pythonrun.c:1357
#38 0x00000000004f7d77 in PyRun_SimpleFileExFlags () at ../Python/pythonrun.c:949
#39 0x00000000004982f2 in Py_Main () at ../Modules/main.c:640
#40 0x00007ffff6f14b45 in __libc_start_main (main=0x497d80 <main>, argc=2, argv=0x7fffffffe568,
init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffe558)
at libc-start.c:287
#41 0x0000000000497ca0 in _start ()
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