Hi all,
I have a galaxy instance running 18.05 version. I recently installed 'suite_samtools_1_2' (revision: 5b673ccc8747). When I used 'Mpileup' tool, I ran into the below error, and the jobs fail.
Error message from UI:
This job was killed when Galaxy was restarted. Please retry the job.
Error report from UI:
python: /home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/galaxy_33.sh: line 61: 27021 Segmentation fault (core dumped) python "/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/set_metadata_16ppzR.py" "/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/registry.xml" "/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/working/galaxy.json" "/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_in_HistoryDatasetAssociation_74_dGoEXq,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_kwds_HistoryDatasetAssociation_74_ZgPen_,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_out_HistoryDatasetAssociation_74_OsySK1,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_results_HistoryDatasetAssociation_74_1NfJC0,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/files/000/dataset_74.dat,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_override_HistoryDatasetAssociation_74_vZTPWp" "/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_in_HistoryDatasetAssociation_75_AoWnZx,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_kwds_HistoryDatasetAssociation_75_J8fJUV,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_out_HistoryDatasetAssociation_75_CXBh3u,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_results_HistoryDatasetAssociation_75_T_tzxr,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/files/000/dataset_75.dat,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_override_HistoryDatasetAssociation_75_9fiQnm" 5242880
From galaxy.log file:
[LocalRunner.work_thread-1] execution finished: /home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/galaxy_33.sh galaxy.model.metadata DEBUG 2018-07-10 17:31:51,417 [p:26910,w:1,m:0] [LocalRunner.work_thread-1] setting metadata externally failed for HistoryDatasetAssociation 74: External set_meta() not called /home/aarthi/GALAXY/galaxy_18/galaxy_18.05/.venv/bin/python: !!! uWSGI process 26910 got Segmentation Fault !!! *** backtrace of 26910 *** /home/aarthi/GALAXY/galaxy_18/galaxy_18.05/.venv/lib/python2.7/site-packages/uwsgi.so(uwsgi_backtrace+0x2e) [0x7fc5c385897e] /home/aarthi/GALAXY/galaxy_18/galaxy_18.05/.venv/lib/python2.7/site-packages/uwsgi.so(uwsgi_segfault+0x2f) [0x7fc5c3858d4f] /lib64/libc.so.6(+0x35270) [0x7fc5ca0ba270] /lib64/libc.so.6(strchrnul+0x1a) [0x7fc5ca11522a] /lib64/libc.so.6(_IO_vfprintf+0x92) [0x7fc5ca0cc212] /lib64/libc.so.6(+0x4c431) [0x7fc5ca0d1431] /lib64/libc.so.6(_IO_vfprintf+0x1ee) [0x7fc5ca0cc36e] /lib64/libc.so.6(+0xf6155) [0x7fc5ca17b155] /lib64/libc.so.6(error+0xcd) [0x7fc5ca17b2ad] /home/aarthi/GALAXY/galaxy_18/galaxy_18.05/.venv/lib/python2.7/site-packages/pysam/./libcbcftools.so(main_vcfindex+0x504) [0x7fc5a9183bc4] /home/aarthi/GALAXY/galaxy_18/galaxy_18.05/.venv/lib/python2.7/site-packages/pysam/libcutils.so(+0x14271) [0x7fc5a96da271] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6722) [0x7fc5cae514e2] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed) [0x7fc5cae53efd] /lib64/libpython2.7.so.1.0(+0x70858) [0x7fc5caddd858] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fc5cadb89a3] /lib64/libpython2.7.so.1.0(+0x5a995) [0x7fc5cadc7995] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fc5cadb89a3] /lib64/libpython2.7.so.1.0(+0xa2ce7) [0x7fc5cae0fce7] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fc5cadb89a3] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x2336) [0x7fc5cae4d0f6] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed) [0x7fc5cae53efd] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x663c) [0x7fc5cae513fc] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed) [0x7fc5cae53efd] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x663c) [0x7fc5cae513fc] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x67bd) [0x7fc5cae5157d] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x67bd) [0x7fc5cae5157d] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed) [0x7fc5cae53efd] /lib64/libpython2.7.so.1.0(+0x7094d) [0x7fc5caddd94d] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fc5cadb89a3] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x17fd) [0x7fc5cae4c5bd] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x67bd) [0x7fc5cae5157d] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x67bd) [0x7fc5cae5157d] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed) [0x7fc5cae53efd] /lib64/libpython2.7.so.1.0(+0x70858) [0x7fc5caddd858] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fc5cadb89a3] /lib64/libpython2.7.so.1.0(+0x5a995) [0x7fc5cadc7995] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fc5cadb89a3] /lib64/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fc5cae4a7b7] /lib64/libpython2.7.so.1.0(+0x1156e2) [0x7fc5cae826e2] /lib64/libpthread.so.0(+0x7e25) [0x7fc5cab58e25] /lib64/libc.so.6(clone+0x6d) [0x7fc5ca17d34d] *** end of backtrace ***
I am testing it inside a virtual box, and currently running galaxy in sudo mode. I saw that galaxy requires 'samtools' to be found in the PATH so, I tried running galaxy like with this command 'sudo env "PATH=$PATH" sh run.sh', still I get the same error.
I will appreciate any help or suggestion. Thanks in advance!
Thanks, Aarthi
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