ctf refinement from a star file containing multiple origin Extract jobs crashes with "RelionError"

[Juraj Ahel]

I recently tried doing some refinements using particles extracted in two separate Extract jobs. Worked well for refinement, but when I tried to proceed to CtfRefinement, I started getting a cryptic error at the "looping through all micrographs" step, which was indicating it's a problem in reading MRC files in the error message.

Tried upgrading to latest version, didn't help.

I checked that all the files referenced in the .star file indeed exist and are valid.

Then I decided to split back the files from the run_data.star of the 3D refinement back into 2 subsets, one for each extract jobs. Ctfrefine now runs successfully on both subsets.

I guess there is some bug coming from the assumption all particle .mrcs files will have the same parent folder?

Best,

Juraj

Error below.

in: /tmp/relion/ja181129_3.0_beta-a7e4b08a67f3/foss-2017a-CUDA-9.1.85/scheres-relion-3.0_beta-a7e4b08a67f3/src/rwMRC.h, line 191
terminate called after throwing an instance of 'RelionError'
[cn-16:00667] *** Process received signal ***
[cn-16:00667] Signal: Aborted (6)
[cn-16:00667] Signal code:  (-6)
[cn-16:00667] [ 0] /lib64/libpthread.so.0(+0xf5e0)[0x2aaaaacde5e0]
[cn-16:00667] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2aaab71f11f7]
[cn-16:00667] [ 2] /lib64/libc.so.6(abort+0x148)[0x2aaab71f28e8]
[cn-16:00667] [ 3] /software/171020/software/gcccore/6.3.0/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x15d)[0x2aaab6dc6f1d]
[cn-16:00667] [ 4] /software/171020/software/gcccore/6.3.0/lib64/libstdc++.so.6(+0x97ed6)[0x2aaab6dc4ed6]
[cn-16:00667] [ 5] /software/171020/software/gcccore/6.3.0/lib64/libstdc++.so.6(+0x96f09)[0x2aaab6dc3f09]
[cn-16:00667] [ 6] /software/171020/software/gcccore/6.3.0/lib64/libstdc++.so.6(__gxx_personality_v0+0x2cd)[0x2aaab6dc485d]
[cn-16:00667] [ 7] /software/171020/software/gcccore/6.3.0/lib64/libgcc_s.so.1(+0xff83)[0x2aaaaac17f83]
[cn-16:00667] [ 8] /software/171020/software/gcccore/6.3.0/lib64/libgcc_s.so.1(_Unwind_Resume+0x57)[0x2aaaaac18487]
[cn-16:00667] [ 9] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi(_ZN5ImageIdE4readERK8FileNameblbb+0x221)[0x467381]
[cn-16:00667] [10] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi[0x4fe000]
[cn-16:00667] [11] /software/171020/software/gcccore/6.3.0/lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x2aaaaabe771f]
[cn-16:00667] [12] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi(_ZN11StackHelper11loadStackFSEPK13MetaDataTableNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiPSt6vectorI21ParFourierTransformerSaISA_EEb+0x132)[0x4f66b2]
[cn-16:00667] [13] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi(_ZN10CtfRefiner24processSubsetMicrographsEll+0x25b)[0x43f29b]
[cn-16:00667] [14] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi(_ZN13CtfRefinerMpi3runEv+0x64)[0x4440f4]
[cn-16:00667] [15] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi(main+0x45)[0x41dee5]
[cn-16:00667] [16] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2aaab71ddc05]
[cn-16:00667] [17] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi[0x41e97f]
[cn-16:00667] *** End of error message ***
in: /tmp/relion/ja181129_3.0_beta-a7e4b08a67f3/foss-2017a-CUDA-9.1.85/scheres-relion-3.0_beta-a7e4b08a67f3/src/rwMRC.h, line 191
terminate called after throwing an instance of 'RelionError'
[cn-15:08456] *** Process received signal ***
[cn-15:08456] Signal: Aborted (6)
[cn-15:08456] Signal code:  (-6)
[cn-15:08456] [ 0] /lib64/libpthread.so.0(+0xf5e0)[0x2aaaaacde5e0]
[cn-15:08456] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2aaab71f11f7]
[cn-15:08456] [ 2] /lib64/libc.so.6(abort+0x148)[0x2aaab71f28e8]
[cn-15:08456] [ 3] /software/171020/software/gcccore/6.3.0/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x15d)[0x2aaab6dc6f1d]
[cn-15:08456] [ 4] /software/171020/software/gcccore/6.3.0/lib64/libstdc++.so.6(+0x97ed6)[0x2aaab6dc4ed6]
[cn-15:08456] [ 5] /software/171020/software/gcccore/6.3.0/lib64/libstdc++.so.6(+0x96f09)[0x2aaab6dc3f09]
[cn-15:08456] [ 6] /software/171020/software/gcccore/6.3.0/lib64/libstdc++.so.6(__gxx_personality_v0+0x2cd)[0x2aaab6dc485d]
[cn-15:08456] [ 7] /software/171020/software/gcccore/6.3.0/lib64/libgcc_s.so.1(+0xff83)[0x2aaaaac17f83]
[cn-15:08456] [ 8] /software/171020/software/gcccore/6.3.0/lib64/libgcc_s.so.1(_Unwind_Resume+0x57)[0x2aaaaac18487]
[cn-15:08456] [ 9] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi(_ZN5ImageIdE4readERK8FileNameblbb+0x221)[0x467381]
[cn-15:08456] [10] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi[0x4fe000]
[cn-15:08456] [11] /software/171020/software/gcccore/6.3.0/lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x2aaaaabe771f]
[cn-15:08456] [12] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi(_ZN11StackHelper11loadStackFSEPK13MetaDataTableNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiPSt6vectorI21ParFourierTransformerSaISA_EEb+0x132)[0x4f66b2]
[cn-15:08456] [13] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi(_ZN10CtfRefiner24processSubsetMicrographsEll+0x25b)[0x43f29b]
[cn-15:08456] [14] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi(_ZN13CtfRefinerMpi3runEv+0x64)[0x4440f4]
[cn-15:08456] [15] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi(main+0x45)[0x41dee5]
[cn-15:08456] [16] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2aaab71ddc05]
[cn-15:08456] [17] /software/extra/EM/software/relion/ja181129_3.0_beta-a7e4b08a67f3-foss-2017a-cuda-9.1.85/bin/relion_ctf_refine_mpi[0x41e97f]
[cn-15:08456] *** End of error message ***

[Takanori Nakane]

Thank you very much for your report. We found the cause. @JZivanov will fix this next week.

[Takanori Nakane]

Hi, could you please try again with our latest commit ced57e0?

[Juraj Ahel]

Hi Takanori, I can't quickly make a new build unfortunately, but I trust that if you could reproduce the problem and have found the issue, that the issue is fixed. Feel free to close the issue.

Best,

Juraj