[galaxy-dev] Error from Bowtie2 parser

31 Jan 2016

      Hello everyone,
I've built a bowtie2 parser for mapping reads back to contigs and while my Python parser works perfectly and even produces the files it's supposed too I get error files from Galaxy (and I've used 2>/dev/null at the end of the command). Even when I used Galaxy's job command line after the tool is finished the tool works but inside galaxy I get the following error:
*** Error in `python': double free or corruption ======= Backtrace: ========= /lib64/libc.so.6(+0x7d1fd)[0x7faab1c5d1fd] /lib64/libc.so.6(fclose+0x155)[0x7faab1c4bae5] /home/galaxy_coverall/galaxy/eggs/pysam-0.4.2_kanwei_b1 /home/galaxy_coverall/galaxy/eggs/pysam-0.4.2_kanwei_b1 /lib64/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7faab2 /lib64/libpython2.7.so.1.0(PyEval_CallObjectWithKeyword /home/galaxy_coverall/galaxy/eggs/pysam-0.4.2_kanwei_b1 /lib64/libpython2.7.so.1.0(+0x9fe13)[0x7faab297fe13] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7faab2 /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x1d4c)[0 /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x7 /lib64/libpython2.7.so.1.0(+0x6f17d)[0x7faab294f17d] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7faab2 /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xde7)[0x /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x4350)[0 /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x4350)[0 /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x7 /lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x7faa /lib64/libpython2.7.so.1.0(+0xfb6cf)[0x7faab29db6cf] /lib64/libpython2.7.so.1.0(PyRun_FileExFlags+0x7e)[0x7f /lib64/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0xe9 /lib64/libpython2.7.so.1.0(Py_Main+0xc9f)[0x7faab29eeb1 /lib64/libc.so.6(__libc_start_main+0xf5)[0x7faab1c01af5 python[0x400721] ======= Memory map: ======== 00400000-00401000 r-xp 00000000 fd:00 134966341 00600000-00601000 r--p 00000000 fd:00 134966341 00601000-00602000 rw-p 00001000 fd:00 134966341 011a1000-064ce000 rw-p 00000000 00:00 0 7faaa15c8000-7faaa15dd000 r-xp 00000000 fd:00 205646465 7faaa15dd000-7faaa17dc000 ---p 00015000 fd:00 205646465 7faaa17dc000-7faaa17dd000 r--p 00014000 fd:00 205646465 7faaa17dd000-7faaa17de000 rw-p 00015000 fd:00 205646465 7faaa17e0000-7faaa1807000 r-xp 00000000 fd:00 201394264 7faaa1807000-7faaa1a07000 ---p 00027000 fd:00 201394264 7faaa1a07000-7faaa1a09000 r--p 00027000 fd:00 201394264 7faaa1a09000-7faaa1a0a000 rw-p 00029000 fd:00 201394264 7faaa1a10000-7faaa1a1b000 r-xp 00000000 fd:00 134861759 7faaa1a1b000-7faaa1c1a000 ---p 0000b000 fd:00 134861759 7faaa1c1a000-7faaa1c1b000 r--p 0000a000 fd:00 134861759 7faaa1c1b000-7faaa1c1d000 rw-p 0000b000 fd:00 134861759 7faaa1c20000-7faaa1c22000 r-xp 00000000 fd:02 423758729 7faaa1c22000-7faaa1d21000 ---p 00002000 fd:02 423758729 7faaa1d21000-7faaa1d22000 rw-p 00001000 fd:02 423758729 7faaa1d28000-7faaa1d32000 r-xp 00000000 fd:02 423758731 7faaa1d32000-7faaa1e32000 ---p 0000a000 fd:02 423758731 7faaa1e32000-7faaa1e33000 rw-p 0000a000 fd:02 423758731 7faaa1e38000-7faaa1e3a000 r-xp 00000000 fd:02 423758730 7faaa1e3a000-7faaa1f39000 ---p 00002000 fd:02 423758730 7faaa1f39000-7faaa1f3a000 rw-p 00001000 fd:02 423758730 7faaa1f40000-7faaa1f43000 r-xp 00000000 fd:02 423758728 7faaa1f43000-7faaa2042000 ---p 00003000 fd:02 423758728 7faaa2042000-7faaa2043000 rw-p 00002000 fd:02 423758728 7faaa2048000-7faaa204a000 r-xp 00000000 fd:02 423758727 7faaa204a000-7faaa2149000 ---p 00002000 fd:02 423758727 7faaa2149000-7faaa214a000 rw-p 00001000 fd:02 423758727 7faaa2150000-7faaa2154000 r-xp 00000000 fd:00 134861771 7faaa2154000-7faaa2353000 ---p 00004000 fd:00 134861771 7faaa2353000-7faaa2354000 r--p 00003000 fd:00 134861771 7faaa2354000-7faaa2356000 rw-p 00004000 fd:00 134861771 7faaa2358000-7faaa235a000 r-xp 00000000 fd:02 423758732 7faaa235a000-7faaa245a000 ---p 00002000 fd:02 423758732 7faaa245a000-7faaa245b000 rw-p 00002000 fd:02 423758732 7faaa2460000-7faaa2466000 r-xp 00000000 fd:00 137235630 7faaa2466000-7faaa2665000 ---p 00006000 fd:00 137235630 7faaa2665000-7faaa2666000 r--p 00005000 fd:00 137235630 7faaa2666000-7faaa2667000 rw-p 00006000 fd:00 137235630 7faaa2668000-7faaa267f000 r-xp 00000000 fd:02 9071725518 7faaa267f000-7faaa277f000 ---p 00017000 fd:02 9071725518 7faaa277f000-7faaa2781000 rw-p 00017000 fd:02 9071725518 7faaa2781000-7faaa2782000 rw-p 00000000 00:00 0 7faaa2788000-7faaa2796000 r-xp 00000000 fd:02 9071725516 7faaa2796000-7faaa2895000 ---p 0000e000 fd:02 9071725516 7faaa2895000-7faaa2897000 rw-p 0000d000 fd:02 9071725516 7faaa2898000-7faaa28a0000 r-xp 00000000 fd:02 9071725515 7faaa28a0000-7faaa29a0000 ---p 00008000 fd:02 9071725515 7faaa29a0000-7faaa29a1000 rw-p 00008000 fd:02 9071725515 7faaa29a8000-7faaa29d3000 r-xp 00000000 fd:02 9071725517 7faaa29d3000-7faaa2ad3000 ---p 0002b000 fd:02 9071725517 7faaa2ad3000-7faaa2ad6000 rw-p 0002b000 fd:02 9071725517 7faaa2ad6000-7faaa2ad7000 rw-p 00000000 00:00 0 7faaa2ad8000-7faaa2ae6000 r-xp 00000000 fd:02 9071725519 7faaa2ae6000-7faaa2be6000 ---p 0000e000 fd:02 9071725519 7faaa2be6000-7faaa2be8000 rw-p 0000e000 fd:02 9071725519 7faaa2be8000-7faaa2be9000 rw-p 00000000 00:00 0 7faaa2bf0000-7faaa2bf7000 r-xp 00000000 fd:00 201393931 7faaa2bf7000-7faaa2df6000 ---p 00007000 fd:00 201393931 7faaa2df6000-7faaa2df7000 r--p 00006000 fd:00 201393931 7faaa2df7000-7faaa2df8000 rw-p 00007000 fd:00 201393931 7faaa2df8000-7faaa2dfa000 r-xp 00000000 fd:02 9072320053 7faaa2dfa000-7faaa2ef9000 ---p 00002000 fd:02 9072320053 7faaa2ef9000-7faaa2efa000 rw-p 00001000 fd:02 9072320053 7faaa2f00000-7faaa2f0a000 r-xp 00000000 fd:02 423762146 7faaa2f0a000-7faaa3009000 ---p 0000a000 fd:02 423762146 7faaa3009000-7faaa300a000 rw-p 00009000 fd:02 423762146 7faaa3010000-7faaa3013000 r-xp 00000000 fd:02 4675969741 7faaa3013000-7faaa3112000 ---p 00003000 fd:02 4675969741 7faaa3112000-7faaa3113000 rw-p 00002000 fd:02 4675969741 7faaa3118000-7faaa3139000 r-xp 00000000 fd:02 423824891 7faaa3139000-7faaa3239000 ---p 00021000 fd:02 423824891 7faaa3239000-7faaa323a000 rw-p 00021000 fd:02 423824891 7faaa3240000-7faaa3248000 r-xp 00000000 fd:02 13260234458 7faaa3248000-7faaa3348000 ---p 00008000 fd:02 13260234458 7faaa3348000-7faaa3349000 rw-p 00008000 fd:02 13260234458 7faaa3350000-7faaa3354000 r-xp 00000000 fd:02 9071725431 7faaa3354000-7faaa3453000 ---p 00004000 fd:02 9071725431 7faaa3453000-7faaa3454000 rw-p 00003000 fd:02 9071725431 7faaa3458000-7faaa3467000 r-xp 00000000 fd:02 4675969882 7faaa3467000-7faaa3567000 ---p 0000f000 fd:02 4675969882 7faaa3567000-7faaa3569000 rw-p 0000f000 fd:02 4675969882 7faaa3570000-7faaa3584000 r-xp 00000000 fd:02 390174777 7faaa3584000-7faaa3683000 ---p 00014000 fd:02 390174777 7faaa3683000-7faaa3686000 rw-p 00013000 fd:02 390174777 7faaa3688000-7faaa36ce000 r-xp 00000000 fd:02 423758022 7faaa36ce000-7faaa37cd000 ---p 00046000 fd:02 423758022 7faaa37cd000-7faaa3802000 rw-p 00045000 fd:02 423758022 7faaa3802000-7faaa3803000 rw-p 00000000 00:00 0 7faaa3808000-7faaa3811000 r-xp 00000000 fd:02 423758008 7faaa3811000-7faaa3910000 ---p 00009000 fd:02 423758008 7fa .. /usr/lib64/libcom_err.so.2.1 7faaa82c3000-7faaa84c2000 ---p 00003000 fd:00 201394128 7faaa84c2000-7faaa84c3000 r--p 00002000 fd:00 201394128 7faaa84c3000-7faaa84c4000 rw-p 00003000 fd:00 201394128 7faaa84c8000-7faaa859b000 r-xp 00000000 fd:00 202456210 7faaa859b000-7faaa879b000 ---p 000d3000 fd:00 202456210 7faaa879b000-7faaa87a8000 r--p 000d3000 fd:00 202456210 7faaa87a8000-7faaa87ab000 rw-p 000e0000 fd:00 202456210 7faaa87b0000-7faaa87f9000 r-xp 00000000 fd:00 202456196 7faaa87f9000-7faaa89f9000 ---p 00049000 fd:00 202456196 7faaa89f9000-7faaa89fa000 r--p 00049000 fd:00 202456196 7faaa89fa000-7faaa89fc000 rw-p 0004a000 fd:00 202456196 7faaa8a00000-7faaa8bbd000 r-xp 00000000 fd:00 206095466 7faaa8bbd000-7faaa8dbd000 ---p 001bd000 fd:00 206095466 7faaa8dbd000-7faaa8dd7000 r--p 001bd000 fd:00 206095466 7faaa8dd7000-7faaa8de3000 rw-p 001d7000 fd:00 206095466 7faaa8de3000-7faaa8de7000 rw-p 00000000 00:00 0 7faaa8de8000-7faaa8e4b000 r-xp 00000000 fd:00 206095468 7faaa8e4b000-7faaa904a000 ---p 00063000 fd:00 206095468 7faaa904a000-7faaa904e000 r--p 00062000 fd:00 206095468 7faaa904e000-7faaa9055000 rw-p 00066000 fd:00 206095468 7faaa9058000-7faaa9060000 r-xp 00000000 fd:00 137235634 7faaa9060000-7faaa925f000 ---p 00008000 fd:00 137235634 7faaa925f000-7faaa9260000 r--p 00007000 fd:00 137235634 7faaa9260000-7faaa9261000 rw-p 00008000 fd:00 137235634 7faaa9268000-7faaa926b000 r-xp 00000000 fd:00 137235621 7faaa926b000-7faaa946a000 ---p 00003000 fd:00 137235621 7faaa946a000-7faaa946b000 r--p 00002000 fd:00 137235621 7faaa946b000-7faaa946c000 rw-p 00003000 fd:00 137235621 7faaa9470000-7faaa947f000 r-xp 00000000 fd:00 137235632 7faaa947f000-7faaa967e000 ---p 0000f000 fd:00 137235632 7faaa967e000-7faaa967f000 r--p 0000e000 fd:00 137235632 7faaa967f000-7faaa9684000 rw-p 0000f000 fd:00 137235632 7faaa9686000-7faaa96c7000 rw-p 00000000 00:00 0 7faaa9788000-7faaa979d000 r-xp 00000000 fd:00 205643504 7faaa979d000-7faaa999c000 ---p 00015000 fd:00 205643504 7faaa999c000-7faaa999d000 r--p 00014000 fd:00 205643504 7faaa999d000-7faaa999e000 rw-p 00015000 fd:00 205643504 7faaa99b8000-7faaa99bc000 r-xp 00000000 fd:00 134861781 7faaa99bc000-7faaa9bbb000 ---p 00004000 fd:00 134861781 7faaa9bbb000-7faaa9bbc000 r--p 00003000 fd:00 134861781 7faaa9bbc000-7faaa9bbe000 rw-p 00004000 fd:00 134861781 7faaa9bc0000-7faaa9bdc000 r-xp 00000000 fd:00 137235625 7faaa9bdc000-7faaa9ddb000 ---p 0001c000 fd:00 137235625 7faaa9ddb000-7faaa9ddc000 r--p 0001b000 fd:00 137235625 7faaa9ddc000-7faaa9de6000 rw-p 0001c000 fd:00 137235625 7faaa9de8000-7faaa9dea000 r-xp 00000000 fd:00 134861735 7faaa9dea000-7faaa9fe9000 ---p 00002000 fd:00 134861735 7faaa9fe9000-7faaa9fea000 r--p 00001000 fd:00 134861735 7faaa9fea000-7faaa9feb000 rw-p 00002000 fd:00 134861735 7faaa9fef000-7faaaa030000 rw-p 00000000 00:00 0 7faaaa030000-7faaaa035000 r-xp 00000000 fd:00 134861768 7faaaa035000-7faaaa234000 ---p 00005000 fd:00 134861768 7faaaa234000-7faaaa235000 r--p 00004000 fd:00 134861768 7faaaa235000-7faaaa237000 rw-p 00005000 fd:00 134861768 7faaaa238000-7faaaa23b000 r-xp 00000000 fd:00 137235623 7faaaa23b000-7faaaa43a000 ---p 00003000 fd:00 137235623 7faaaa43a000-7faaaa43b000 r--p 00002000 fd:00 137235623 7faaaa43b000-7faaaa43d000 rw-p 00003000 fd:00 137235623 7faaaa440000-7faaaa44a000 r-xp 00000000 fd:00 134861739 7faaaa44a000-7faaaa649000 ---p 0000a000 fd:00 134861739 7faaaa649000-7faaaa64a000 r--p 00009000 fd:00 134861739 7faaaa64a000-7faaaa64f000 rw-p 0000a000 fd:00 134861739 7faaaa650000-7faaaa658000 r-xp 00000000 fd:00 134861755 7faaaa658000-7faaaa858000 ---p 00008000 fd:00 134861755 7faaaa858000-7faaaa859000 r--p 00008000 fd:00 134861755 7faaaa859000-7faaaa85b000 rw-p 00009000 fd:00 134861755 7faaaa860000-7faaaa866000 r-xp 00000000 fd:00 134861692 7faaaa866000-7faaaaa65000 ---p 00006000 fd:00 134861692 7faaaaa65000-7faaaaa66000 r--p 00005000 fd:00 134861692 7faaaaa66000-7faaaaa68000 rw-p 00006000 fd:00 134861692 7faaaaa68000-7faaaaa6c000 r-xp 00000000 fd:00 134861772 7faaaaa6c000-7faaaac6b000 ---p 00004000 fd:00 134861772 7faaaac6b000-7faaaac6c000 r--p 00003000 fd:00 134861772 7faaaac6c000-7faaaac6e000 rw-p 00004000 fd:00 134861772 7faaaac70000-7faaaac75000 r-xp 00000000 fd:00 137235638 7faaaac75000-7faaaae74000 ---p 00005000 fd:00 137235638 7faaaae74000-7faaaae75000 r--p 00004000 fd:00 137235638 7faaaae75000-7faaaae76000 rw-p 00005000 fd:00 137235638 7faaaae78000-7faaaae80000 r-xp 00000000 fd:00 137235626 7faaaae80000-7faaab07f000 ---p 00008000 fd:00 137235626 7faaab07f000-7faaab080000 r--p 00007000 fd:00 137235626 7faaab080000-7faaab081000 rw-p 00008000 fd:00 137235626 7faaab088000-7faaab08f000 r-xp 00000000 fd:00 137235635 7faaab08f000-7faaab28e000 ---p 00007000 fd:00 137235635 7faaab28e000-7faaab28f000 r--p 00006000 fd:00 137235635 7faaab28f000-7faaab291000 rw-p 00007000 fd:00 137235635 7faaab298000-7faaab29c000 r-xp 00000000 fd:00 137235641 7faaab29c000-7faaab49b000 ---p 00004000 fd:00 137235641 7faaab49b000-7faaab49c000 r--p 00003000 fd:00 137235641 7faaab49c000-7faaab49e000 rw-p 00004000 fd:00 137235641 7faaab4a0000-7faaab4b2000 r-xp 00000000 fd:00 137235640 7faaab4b2000-7faaab6b2000 ---p 00012000 fd:00 137235640 7faaab6b2000-7faaab6b3000 r--p 00012000 fd:00 137235640 7faaab6b3000-7faaab6b4000 rw-p 00013000 fd:00 137235640 7faaab6b8000-7faab1bdf000 r--p 00000000 fd:00 201393959 7faab1be0000-7faab1d96000 r-xp 00000000 fd:00 201393901 7faab1d96000-7faab1f96000 ---p 001b6000 fd:00 201393901 7faab1f96000-7faab1f9a000 r--p 001b6000 fd:00 201393901 7faab1f9a000-7faab1f9c000 rw-p 001ba000 fd:00 201393901 7faab1f9c000-7faab1fa1000 rw-p 00000000 00:00 0 7faab1fa8000-7faab20a9000 r-xp 00000000 fd:00 201393909 7faab20a9000-7faab22a8000 ---p 00101000 fd:00 201393909 7faab22a8000-7faab22a9000 r--p 00100000 fd:00 201393909 7faab22a9000-7faab22aa000 rw-p 00101000 fd:00 201393909 7faab22b0000-7faab22b2000 r-xp 00000000 fd:00 201393935 7faab22b2000-7faab24b1000 ---p 00002000 fd:00 201393935 7faab24b1000-7faab24b2000 r--p 00001000 fd:00 201393935 7faab24b2000-7faab24b3000 rw-p 00002000 fd:00 201393935 7faab24b8000-7faab24bb000 r-xp 00000000 fd:00 201393907 7faab24bb000-7faab26ba000 ---p 00003000 fd:00 201393907 7faab26ba000-7faab26bb000 r--p 00002000 fd:00 201393907 7faab26bb000-7faab26bc000 rw-p 00003000 fd:00 201393907 7faab26c0000-7faab26d6000 r-xp 00000000 fd:00 201393927 7faab26d6000-7faab28d6000 ---p 00016000 fd:00 201393927 7faab28d6000-7faab28d7000 r--p 00016000 fd:00 201393927 7faab28d7000-7faab28d8000 rw-p 00017000 fd:00 201393927 7faab28d8000-7faab28dc000 rw-p 00000000 00:00 0 7faab28e0000-7faab2a58000 r-xp 00000000 fd:00 206021639 7faab2a58000-7faab2c58000 ---p 00178000 fd:00 206021639 7faab2c58000-7faab2c59000 r--p 00178000 fd:00 206021639 7faab2c59000-7faab2c97000 rw-p 00179000 fd:00 206021639 7faab2c97000-7faab2ca6000 rw-p 00000000 00:00 0 7faab2ca8000-7faab2cc9000 r-xp 00000000 fd:00 201393894 7faab2ccd000-7faab2e12000 rw-p 00000000 00:00 0 7faab2e41000-7faab2ec9000 rw-p 00000000 00:00 0 7faab2ec9000-7faab2eca000 r--p 00021000 fd:00 201393894 7faab2eca000-7faab2ecb000 rw-p 00022000 fd:00 201393894 7faab2ecb000-7faab2ecd000 rw-p 00000000 00:00 0 7faab2ecd000-7faab2ecf000 rw-p 00000000 00:00 0 7ffc473a7000-7ffc473c9000 rw-p 00000000 00:00 0 7ffc473e0000-7ffc473e2000 r-xp 00000000 00:00 0 ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 /home/galaxy_coverall/galaxy/database/job_working_direc My parser does the following: 1) Creates a sam file from an already indexed 2) Calls samtools to create the appropriate bam file 3) Calls samtools again to create the appropriate

(!prev): 0x0000000002debfc0 *** 0f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(bam_index_load_literal+0x37)[0x7faaa43c2ad7] 0f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(+0x6e7f8)[0x7faaa43ae7f8] 92a073] s+0x47)[0x7faab29bbfd7] 0f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(+0x52a04)[0x7faaa4392a04] 92a073] x7faab29be32c] faab29c218d] 92a073] 7faab29bd3c7] x7faab29c0930] x7faab29c0930] faab29c218d] b29c2292] aab29dc88e] )[0x7faab29ddb19] f] ] /usr/bin/python2.7 /usr/bin/python2.7 /usr/bin/python2.7 [heap] /usr/lib64/libgcc_s-4.8.5-20150702.so.1 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 /usr/lib64/libexpat.so.1.6.0 /usr/lib64/libexpat.so.1.6.0 /usr/lib64/libexpat.so.1.6.0 /usr/lib64/libexpat.so.1.6.0 /usr/lib64/python2.7/lib-dynload/pyexpat.so /usr/lib64/python2.7/lib-dynload/pyexpat.so /usr/lib64/python2.7/lib-dynload/pyexpat.so /usr/lib64/python2.7/lib-dynload/pyexpat.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/diffhelpers.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/diffhelpers.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/diffhelpers.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/parsers.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/parsers.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/parsers.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/mpatch.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/mpatch.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/mpatch.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/bdiff.so 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/usr/lib64/python2.7/lib-dynload/_heapq.so /usr/lib64/python2.7/lib-dynload/_heapq.so /usr/lib64/python2.7/lib-dynload/itertoolsmodule.so /usr/lib64/python2.7/lib-dynload/itertoolsmodule.so /usr/lib64/python2.7/lib-dynload/itertoolsmodule.so /usr/lib64/python2.7/lib-dynload/itertoolsmodule.so /usr/lib64/python2.7/lib-dynload/operator.so /usr/lib64/python2.7/lib-dynload/operator.so /usr/lib64/python2.7/lib-dynload/operator.so /usr/lib64/python2.7/lib-dynload/operator.so /usr/lib64/python2.7/lib-dynload/_collectionsmodule.so /usr/lib64/python2.7/lib-dynload/_collectionsmodule.so /usr/lib64/python2.7/lib-dynload/_collectionsmodule.so /usr/lib64/python2.7/lib-dynload/_collectionsmodule.so /usr/lib64/python2.7/lib-dynload/timemodule.so /usr/lib64/python2.7/lib-dynload/timemodule.so /usr/lib64/python2.7/lib-dynload/timemodule.so /usr/lib64/python2.7/lib-dynload/timemodule.so /usr/lib64/python2.7/lib-dynload/binascii.so /usr/lib64/python2.7/lib-dynload/binascii.so /usr/lib64/python2.7/lib-dynload/binascii.so /usr/lib64/python2.7/lib-dynload/binascii.so /usr/lib64/python2.7/lib-dynload/_json.so /usr/lib64/python2.7/lib-dynload/_json.so /usr/lib64/python2.7/lib-dynload/_json.so /usr/lib64/python2.7/lib-dynload/_json.so /usr/lib64/python2.7/lib-dynload/_struct.so /usr/lib64/python2.7/lib-dynload/_struct.so /usr/lib64/python2.7/lib-dynload/_struct.so /usr/lib64/python2.7/lib-dynload/_struct.so /usr/lib64/python2.7/lib-dynload/cStringIO.so /usr/lib64/python2.7/lib-dynload/cStringIO.so /usr/lib64/python2.7/lib-dynload/cStringIO.so /usr/lib64/python2.7/lib-dynload/cStringIO.so /usr/lib64/python2.7/lib-dynload/cPickle.so /usr/lib64/python2.7/lib-dynload/cPickle.so /usr/lib64/python2.7/lib-dynload/cPickle.so /usr/lib64/python2.7/lib-dynload/cPickle.so /usr/lib/locale/locale-archive /usr/lib64/libc-2.17.so /usr/lib64/libc-2.17.so /usr/lib64/libc-2.17.so /usr/lib64/libc-2.17.so /usr/lib64/libm-2.17.so /usr/lib64/libm-2.17.so /usr/lib64/libm-2.17.so /usr/lib64/libm-2.17.so /usr/lib64/libutil-2.17.so /usr/lib64/libutil-2.17.so /usr/lib64/libutil-2.17.so /usr/lib64/libutil-2.17.so /usr/lib64/libdl-2.17.so /usr/lib64/libdl-2.17.so /usr/lib64/libdl-2.17.so /usr/lib64/libdl-2.17.so /usr/lib64/libpthread-2.17.so /usr/lib64/libpthread-2.17.so /usr/lib64/libpthread-2.17.so /usr/lib64/libpthread-2.17.so /usr/lib64/libpython2.7.so.1.0 /usr/lib64/libpython2.7.so.1.0 /usr/lib64/libpython2.7.so.1.0 /usr/lib64/libpython2.7.so.1.0 /usr/lib64/ld-2.17.so /usr/lib64/ld-2.17.so /usr/lib64/ld-2.17.so [stack] [vdso] [vsyscall] tory2/000/30/galaxy_30.sh: line 21: 38559 Aborted                 (core dumped) python "/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/set_metadata_CkVy0K.py" "/home/galaxy_coverall/galaxy/database/tmp/tmpKjfqUF" "/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/galaxy.json" "/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_in_HistoryDatasetAssociation_49_0OTW3F,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_kwds_HistoryDatasetAssociation_49_HjgVuR,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_out_HistoryDatasetAssociation_49_on8AdF,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_results_HistoryDatasetAssociation_49_CnZVLx,/home/galaxy_coverall/galaxy/database/files2/001/dataset_1739.dat,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_override_HistoryDatasetAssociation_49_KSfIN1" "/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_in_HistoryDatasetAssociation_50_hwtfVm,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_kwds_HistoryDatasetAssociation_50_h1vk_m,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_out_HistoryDatasetAssociation_50_nT4xXj,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_results_HistoryDatasetAssociation_50_KaNi5o,/home/galaxy_coverall/galaxy/database/files2/001/dataset_1740.dat,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_override_HistoryDatasetAssociation_50_CHPwpR" "/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_in_HistoryDatasetAssociation_51_qFch9V,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_kwds_HistoryDatasetAssociation_51__ijkKo,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_out_HistoryDatasetAssociation_51_zvlnQn,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_results_HistoryDatasetAssociation_51_UhLJnu,/home/galaxy_coverall/galaxy/database/files2/001/dataset_1741.dat,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_override_HistoryDatasetAssociation_51_4t9S_g" 5242880 contig file sorted bam file
I've commented the steps one by one and the problem starts at the mapping (even though the scripts does continue to work and produces the files it's supposed too in the 'database/files/' directory)
Has anyone encountered something like that before?
Kind regards,
Makis Ladoukakis

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[galaxy-dev] Error from Bowtie2 parser