Error with SAMTools Mpileup v1.2

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Error with SAMTools Mpileup v1.2

Aarthi Mohan-2

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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