relion_helix_toolbox doesn't work #122

bforsbe · 2016-10-10T08:50:12Z

Originally reported by: Jing_basel (Bitbucket: Jing_basel, GitHub: Unknown)

Dear all,
I would like to use the region_helix_tool box to get rid of some particles with huge out of plane tilt angle and soon I realised no matter what I type after the "region_helix_toolbox" command, it always prints out a list of options followed by the same error message:

Only one option can be specified at one time! valid_options = 127
File: /scicore/home/basler/wangji/src/relion2.0beta/src/apps/helix_toolbox.cpp line: 294

Is there something specific need to be done to compile the helix_tool box? There are plenty nice options of this tool box, it would be great to have it work.

Thanks a lot,

Jing

Bitbucket: https://bitbucket.org/tcblab/relion2-beta/issue/122

bforsbe · 2016-10-12T11:13:40Z

Original comment by Sjors Scheres (Bitbucket: scheres, GitHub: scheres):

What was the command line used?

bforsbe · 2016-10-12T19:24:44Z

Original comment by Jing_basel (Bitbucket: Jing_basel, GitHub: Unknown):

Hi Sjors,

I trired:

"relion_helix_toolbox"
or
"relion_helix_toolbox --help"

I got the same error message:

Only one option can be specified at one time! valid_options = 127
File: /scicore/pfs/mcleod/relion2-beta/src/apps/helix_toolbox.cpp line: 294

When I tried:
relion_helix_toolbox --cylinder --o ref.mrc --boxdim 300 --cyl_outer_diameter 200 --angpix 1.34

The error message is slightly difference:

Only one option can be specified at one time! valid_options = 128
File: /scicore/pfs/mcleod/relion2-beta/src/apps/helix_toolbox.cpp line: 294

Is there a command to test if the relion_helix_toolbox is installed properly?

Thanks a lot for your help!

Jing

bforsbe · 2016-10-12T19:50:08Z

Original comment by Sjors Scheres (Bitbucket: scheres, GitHub: scheres):

It is installed correctly, you're not using it correctly. See the helical
page on the relion wiki for some examples on how to use the program. It
can do many things, but admittedly the documentation isn't great yet.
HTH,
Sjors

bforsbe · 2016-10-12T20:46:33Z

Original comment by Jing_basel (Bitbucket: Jing_basel, GitHub: Unknown):

Hi Sjors,

I also tried the examples copied from the wiki page:

relion_helix_toolbox --cylinder --o ref.mrc --boxdim 300 --cyl_outer_diameter 200 --cyl_inner_diameter -1 --angpix 1.34 --sphere_percentage 0.9 --width 5

relion_helix_toolbox --simulate_helix --o VipASimRefCyl160Sub80.mrc --subunit_diameter 80 --cyl_outer_diameter 160 --angpix 1 --rise 21.8 --twist 29.41 --boxdim 450 --sym_Cn 6 --sphere_percentage 0.9 --width 5

Still got the same error message.

From what I understand of the wiki page:
"Type the command relion_helix_toolbox [function] --help for the usage of a function."
The command to see the usage of function "cylinder" is:

relion_helix_toolbox [cylinder] --help

And I also tried:

relion_helix_toolbox cylinder --help

relion_helix_toolbox --help cylinder

Still not working : (

Do you mind just showing me what's the correct command to get this "help" option work?

Thanks a lot!

Jing

bforsbe · 2016-10-13T06:20:07Z

Original comment by Sjors Scheres (Bitbucket: scheres, GitHub: scheres):

relion_helix_toolbox --cylinder --help
should do it.
S

bforsbe · 2016-10-13T08:21:04Z

Original comment by Jing_basel (Bitbucket: Jing_basel, GitHub: Unknown):

Hi Sjors,

Thanks for your reply!

I tried the command:
relion_helix_toolbox --cylinder --help

Still got the same error message:

Only one option can be specified at one time! valid_options = 128
File: /scicore/pfs/mcleod/relion2-beta/src/apps/helix_toolbox.cpp line: 294

Maybe it's a c++ compiling issue?
Anyway the rest of the relion helical processing works great, thanks a lot for your your effort to incorporate the helical module to relion!
Jing

bforsbe · 2016-10-13T10:37:06Z

Original comment by Shaoda He (Bitbucket: sh802, GitHub: sh802):

Dear Jing,
I have made the following changes to src/apps/helix_toolbox.cpp (lines 266-289). Please replace these lines with the code below, recompile and see if the error message is still there. (I suspect that the old-style type cast statements cause trouble.)

	valid_options += (do_extract_coords_relion) ? (1) : (0);
	valid_options += (do_extract_coords_ximdisp) ? (1) : (0);
	valid_options += (do_extract_coords_eman) ? (1) : (0);
	valid_options += (do_convert_coords_emn2rln) ? (1) : (0);
	valid_options += (do_convert_coords_xim2rln) ? (1) : (0);
	valid_options += (do_combine_GCTF_results) ? (1) : (0);
	valid_options += (do_apply_spherical_mask_3D) ? (1) : (0);
	valid_options += (do_crop_central_Z) ? (1) : (0);
	valid_options += (do_create_cylinder_3D) ? (1) : (0);
	valid_options += (do_set_default_tilt) ? (1) : (0);
	valid_options += (do_remove_segments_with_bad_tilt) ? (1) : (0);
	valid_options += (do_remove_segments_with_bad_psi) ? (1) : (0);
	valid_options += (do_remove_mics_with_bad_ctf) ? (1) : (0);
	valid_options += (do_simulate_helix_3D) ? (1) : (0);
	valid_options += (do_impose_helical_symmetry) ? (1) : (0);
	valid_options += (do_local_search_helical_symmetry) ? (1) : (0);
	valid_options += (do_PDB_helix) ? (1) : (0);
	valid_options += (do_divide_star_file) ? (1) : (0);
	valid_options += (do_merge_star_files) ? (1) : (0);
	valid_options += (do_sort_datastar_tubeID) ? (1) : (0);
	valid_options += (do_simulate_helical_segments_2D) ? (1) : (0);
	valid_options += (do_cut_out) ? (1) : (0);
	valid_options += (do_set_xmipp_origin) ? (1) : (0);

// valid_options += (do_impose_helical_symmetry_fourier_space) ? (1) : (0);

Best,

Shaoda

bforsbe · 2016-10-13T12:31:59Z

Original comment by Jing_basel (Bitbucket: Jing_basel, GitHub: Unknown):

Hi Shaoda,

Thanks a lot for your suggestion!
Replacing the code didn't solve the problem, but by commenting out line 276 to 289 at least allow the options specified from line 265 to 275 to work.

//valid_options += (do_remove_segments_with_bad_psi) ? (1) : (0);
//valid_options += (do_remove_mics_with_bad_ctf) ? (1) : (0);
//valid_options += (do_simulate_helix_3D) ? (1) : (0);
//valid_options += (do_impose_helical_symmetry) ? (1) : (0);
//valid_options += (do_local_search_helical_symmetry) ? (1) : (0);
//valid_options += (do_PDB_helix) ? (1) : (0);
//valid_options += (do_divide_star_file) ? (1) : (0);
//valid_options += (do_merge_star_files) ? (1) : (0);
//valid_options += (do_sort_datastar_tubeID) ? (1) : (0);
//valid_options += (do_simulate_helical_segments_2D) ? (1) : (0);
//valid_options += (do_cut_out) ? (1) : (0);
//valid_options += (do_set_xmipp_origin) ? (1) : (0);
//valid_options += (do_impose_helical_symmetry_fourier_space) ? (1) : (0);

I'm not familiar with c++, but it seems like some of those options are set to true by default?

Jing

bforsbe · 2016-10-13T23:22:33Z

Original comment by Shaoda He (Bitbucket: sh802, GitHub: sh802):

Hi Jing. I am happy that you can use the options you want. But I think the bug still exists and everything seems fine with our compiler. Could you do me a favour? Could you replace "src/apps/helix_toolbox.cpp" with this one: ftp://ftp.mrc-lmb.cam.ac.uk/pub/she/2016-10-13/helix_toolbox.cpp , recompile and type in the command "relion_helix_toolbox --help" ? There should be an additional line before the error message:
Valid options = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
Could you copy the numbers you have to me? And you may also try options without any parameters: e.g. "relion_helix_toolbox --help --remove_bad_tilt", and the line before the error message should look like:
Valid options = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1
If the numbers grow to ~127, then there is a need to investigate which option leads to a very large number by typing in the options one by one and checking the numbers. It will require some work and I truly appreciate if you could help us and the users with a similar compiler as yours to fix that bug. Thanks.

Best,

Shaoda

bforsbe · 2016-10-14T13:16:04Z

Original comment by Jing_basel (Bitbucket: Jing_basel, GitHub: Unknown):

Hi Shaoda,
The compilation failed at the new helix_toolbox.cpp:

/scicore/home/basler/wangji/src/relion2.0beta/src/apps/helix_toolbox.cpp: In member function ‘void helix_bilder_parameters::run()’:
/scicore/home/basler/wangji/src/relion2.0beta/src/apps/helix_toolbox.cpp:644:47: error: too many arguments to function ‘bool localSearchHelicalSymmetry(const MultidimArray&, double, double, double, double, double, double, double, double, double&, double, double, double, double&)’
((verb == true) ? (&std::cout) : (NULL)) );
^
In file included from /scicore/home/basler/wangji/src/relion2.0beta/src/apps/helix_toolbox.cpp:22:0:
/scicore/home/basler/wangji/src/relion2.0beta/src/helix.h:90:6: note: declared here
bool localSearchHelicalSymmetry(
^
make[2]: *** [src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o] Error 1
make[1]: *** [src/apps/CMakeFiles/helix_toolbox.dir/all] Error 2

###

How to upload a txt file to this forum? or do you have another email address so that I can send you the cmakeoutput.log and cmakeerror.log?

Thanks,

Jing

bforsbe · 2016-10-14T14:32:29Z

Original comment by Jing_basel (Bitbucket: Jing_basel, GitHub: Unknown):

Alright, the culprit is option "do_remove_mics_with_bad_ctf". I added a line to print the value of valid_options after each valid_option += xxxxx and here's the output:

[wangji@login11 contracted_2aa]$ relion_helix_toolbox --help

valid_options_psi = 0
valid_options_ctf = 127
valid_options_simulate = 127
valid_options_impose = 127
valid_options_local = 127
valid_options_pdb = 127
valid_options_divid = 127
valid_options_merge = 127
valid_options_sort = 127
valid_options_silulate = 127
valid_options_cut = 127
valid_options_set = 127

Once I commented out the ctf thingy, which is actually not listed in the helix_toolbox functions:
//valid_options += (do_remove_mics_with_bad_ctf) ? (1) : (0);

Everything else seems fine:
[wangji@login11 contracted_2aa]$ relion_helix_toolbox --help
valid_options_psi = 0
valid_options_simulate = 0
valid_options_impose = 0
valid_options_local = 0
valid_options_pdb = 0
valid_options_divid = 0
valid_options_merge = 0
valid_options_sort = 0
valid_options_silulate = 0
valid_options_cut = 0
valid_options_set = 0

Jing

bforsbe · 2016-10-17T16:57:27Z

Original comment by Shaoda He (Bitbucket: sh802, GitHub: sh802):

Hi Jing, I am sorry for replying late. Good spot! That's my fault. Thanks for helping us solve the problem. Could you try compiling this file: ftp://ftp.mrc-lmb.cam.ac.uk/pub/she/2016-10-17/helix_toolbox.cpp ? I think everything should be fine now.

Best,

Shaoda

bforsbe · 2016-10-17T19:08:21Z

Original comment by Jing_basel (Bitbucket: Jing_basel, GitHub: Unknown):

Hi Shaoda,

Thank you very much for fixing the code! The new helix_toolbox.cpp file works quite well except just one more problem that I found: the "remove_bad_ctf" doesn't take the arg of "--EPA_lowest_res", alone or after "--ctf_fom_min".

I had a look through the input data.star file and the "_rlnCtfMaxResolution #21" ranges from 3-5 A. However no particle was removed by the relion_helix_tool --EPA_lowest_res criteria.

Here's the result of a few tests:

[wangji@login11 fourth_round]$ relion_helix_toolbox --remove_bad_ctf --i run_data.star --o out.star --ctf_fom_min 0.1
Number of micrographs (input / output) = 6324 / 1772

[wangji@login11 fourth_round]$ relion_helix_toolbox --remove_bad_ctf --i run_data.star --o out.star --EPA_lowest_res 5
Number of micrographs (input / output) = 6324 / 6324

[wangji@login11 fourth_round]$ relion_helix_toolbox --remove_bad_ctf --i run_data.star --o out.star --EPA_lowest_res 4
Number of micrographs (input / output) = 6324 / 6324

[wangji@login11 fourth_round]$ relion_helix_toolbox --remove_bad_ctf --i run_data.star --o out.star --EPA_lowest_res 3
Number of micrographs (input / output) = 6324 / 6324

[wangji@login11 fourth_round]$ relion_helix_toolbox --remove_bad_ctf --i run_data.star --o out.star --EPA_lowest_res 2
Number of micrographs (input / output) = 6324 / 6324

[wangji@login11 fourth_round]$ relion_helix_toolbox --remove_bad_ctf --i run_data.star --o
out.star --EPA_lowest_res 1
Number of micrographs (input / output) = 6324 / 6324

[wangji@login11 fourth_round]$ relion_helix_toolbox --remove_bad_ctf --i run_data.star --o out.star --ctf_fom_min 0.1 --o out.star --EPA_lowest_res 4
Number of micrographs (input / output) = 6324 / 1772

It would be great to have that option works, so that I don't need to manually remove all the micro-graphs with bad ctf.

Thanks a lot,

Jing

bforsbe · 2016-10-17T23:46:30Z

Original comment by Shaoda He (Bitbucket: sh802, GitHub: sh802):

Hi Jing. Thanks for testing this option. I haven't found the bug by myself because I always use "subset selection" (relion_display) to get rid of the bad micrographs after CTF correction. We encourage users to work inside pipelines whenever possible. Anyway, please copy the file: ftp://ftp.mrc-lmb.cam.ac.uk/pub/she/src/helix.cpp to your "src" directory and try again.

Best,
Shaoda

bforsbe · 2016-10-18T09:06:18Z

Original comment by Jing_basel (Bitbucket: Jing_basel, GitHub: Unknown):

Hi Shaodao,

Thanks for the update! The new helix.cpp caused an installation error:

[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//pipeliner.cpp.o
/scicore/home/basler/wangji/src/relion2.0beta/src/helix.cpp: In function ‘void convertHelicalTubeCoordsToMetaDataTable(FileName&, MetaDataTable&, int&, int&, int, double, double, double, double, double, bool, bool)’:
/scicore/home/basler/wangji/src/relion2.0beta/src/helix.cpp:1596:48: error: ‘EMDL_PARTICLE_HELICAL_TUBE_PITCH’ was not declared in this scope
bool MDin_has_pitch = MD_in.containsLabel(EMDL_PARTICLE_HELICAL_TUBE_PITCH);
^
[ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//complex.cpp.o
make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/apps/CMakeFiles/relion_lib.dir/all] Error 2
make: *** [all] Error 2

Is it an easy fix? Otherwise I'll just use the subset selection to discard micrographs.

Cheers,

Jing

bforsbe · 2016-10-18T10:47:57Z

Original comment by Shaoda He (Bitbucket: sh802, GitHub: sh802):

Hi Jing, I am sorry that we have very different versions of RELION 2.0. Although this problem can be fixed by replacing "metadata_label.h", I don't want you to do that because it risks messing up other parts of the program. Could you try the old "helix.cpp" file with modified "void excludeLowCTFCCMicrographs()" function?

void excludeLowCTFCCMicrographs(
FileName& fn_in,
FileName& fn_out,
RFLOAT cc_min,
RFLOAT EPA_lowest_res)
{
bool contain_EPA_res;
MetaDataTable MD_in, MD_out;
int nr_mics_old, nr_mics_new;
RFLOAT cc, EPA_res;
if ( (fn_in.getFileFormat() != "star") || (fn_out.getFileFormat() != "star") )
REPORT_ERROR("helix.cpp::excludeLowCTFCCMicrographs(): MetaDataTable should have .star extension.");
if (fn_in == fn_out)
REPORT_ERROR("helix.cpp::excludeLowCTFCCMicrographs(): File names must be different.");

MD_in.clear();
MD_in.read(fn_in);
if ( (!MD_in.containsLabel(EMDL_CTF_DEFOCUSU))
		|| (!MD_in.containsLabel(EMDL_CTF_DEFOCUSV))
		|| (!MD_in.containsLabel(EMDL_CTF_DEFOCUS_ANGLE))
		|| (!MD_in.containsLabel(EMDL_CTF_VOLTAGE))
		|| (!MD_in.containsLabel(EMDL_CTF_CS))
		|| (!MD_in.containsLabel(EMDL_CTF_Q0))
		|| (!MD_in.containsLabel(EMDL_CTF_MAGNIFICATION))
		|| (!MD_in.containsLabel(EMDL_CTF_DETECTOR_PIXEL_SIZE))
		|| (!MD_in.containsLabel(EMDL_CTF_FOM)) )
	REPORT_ERROR("helix.cpp::removeBadTiltParticlesFromDataStar(): Input STAR file should contain CTF information.");

contain_EPA_res = MD_in.containsLabel(EMDL_CTF_MAXRES);

nr_mics_old = nr_mics_new = 0;
MD_out.clear();
FOR_ALL_OBJECTS_IN_METADATA_TABLE(MD_in)
{
	nr_mics_old++;
	MD_in.getValue(EMDL_CTF_FOM, cc);
	MD_in.getValue(EMDL_CTF_MAXRES, EPA_res);
	if (cc > cc_min)
	{
		if ( (contain_EPA_res) && (EPA_res > EPA_lowest_res) )
		{}
		else
		{
			nr_mics_new++;
			MD_out.addObject(MD_in.getObject());
		}
	}
}

std::cout << " Number of micrographs (input / output) = " << nr_mics_old << " / " << nr_mics_new << std::endl;
if (MD_out.numberOfObjects() < 1)
	std::cout << " No micrographs in output file!" << std::endl;

MD_out.write(fn_out);
return;

}

Best,

Shaoda

bforsbe · 2016-10-18T10:49:34Z

Original comment by Shaoda He (Bitbucket: sh802, GitHub: sh802):

Hi Jing. The modified function can also be found at: ftp://ftp.mrc-lmb.cam.ac.uk/pub/she/src/modified.txt

bforsbe · 2016-10-18T13:18:26Z

Original comment by Jing_basel (Bitbucket: Jing_basel, GitHub: Unknown):

Hi Shaoda,
I replaced the "void excludeLowCTFCCMicrographs()" function of the original helix.cpp with the modified version, still the "--epa_lowest_res" option is ignored.

[wangji@login11 fourth_round]$ relion_helix_toolbox --remove_bad_ctf --i run_data.star --o test.star --EPA_lowest_res 3
Number of micrographs (input / output) = 6324 / 6324

Sorry about this back and forth, maybe I'll just wait for the new version of Relion2.

Cheers,

Jing

bforsbe · 2016-10-18T14:15:30Z

Original comment by Shaoda He (Bitbucket: sh802, GitHub: sh802):

Hi Jing, I am sorry that with so many versions of RELION 2.0 around I don't know exactly what you have. Could you send the input file ("run_data.star"???, you may compress the file if it is too large) and the commands to me by email (sh802@cam.ac.uk or she@mrc-lmb.cam.ac.uk) ? If the option in my version works, I suggest that you just wait for the next public release of RELION 2.0 and select subsets with the GUI for the moment :)
Best,

Shaoda

bforsbe · 2016-10-18T15:36:32Z

Original comment by Shaoda He (Bitbucket: sh802, GitHub: sh802):

Hi Jing. Thanks for your email. I have performed tests on your STAR file and the results are stored in: ftp://ftp.mrc-lmb.cam.ac.uk/pub/she/helix/jing (commands and the screen output are copied to "notes" file). I think my version works well. And additional tests using my STAR file have also been done: ftp://ftp.mrc-lmb.cam.ac.uk/pub/she/helix/shaoda (Now I have added new parameters "--df_min" and "--df_max"). I guess we might have different set of EMDL labels. If you are still interested in what happened, could you send "src/metadata_label.h" to me by email? Or you may just wait for the next release of RELION :)

I also suggest that micrographs (with their CTF information estimated), not extracted particles, should be selected with "helix_toolbox --remove_bad_ctf". And it is encouraged to select subsets in the GUI if you don't have complicated selection criteria.

Best,

Shaoda

munanbt2004 · 2017-10-31T03:12:54Z

Hi,
I was trying to run a 2D class average in relion using GPU acceleration. I am getting this following error. Any idea what I am doing wrong.

ERROR: unknown error in /programs/x86_64-linux/relion/2.1b1_cu8.0/src/gpu_utils/cuda_projector.cu at line 126 (error-code 30)
[bc-gpu1:05575] *** Process received signal ***
[bc-gpu1:05575] Signal: Segmentation fault (11)
[bc-gpu1:05575] Signal code: (-6)
[bc-gpu1:05575] Failing at address: 0x82ab000015c7
[bc-gpu1:05575] [ 0] /lib64/libpthread.so.0(+0xf5e0)[0x2b64806745e0]
[bc-gpu1:05575] [ 1] /lib64/libpthread.so.0(raise+0x2b)[0x2b64806744ab]
[bc-gpu1:05575] [ 2] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_gpu_util.so(_ZN13CudaProjector9setMdlDimEiiiiiii+0x5bb)[0x2b647f51e20b]
[bc-gpu1:05575] [ 3] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_gpu_util.so(_ZN14MlDeviceBundle22setupFixedSizedObjectsEv+0x252)[0x2b647f525c52]
[bc-gpu1:05575] [ 4] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_lib.so(_ZN14MlOptimiserMpi11expectationEv+0x118d)[0x2b64756f344d]
[bc-gpu1:05575] [ 5] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_lib.so(_ZN14MlOptimiserMpi7iterateEv+0x96)[0x2b64757014f6]
[bc-gpu1:05575] [ 6] /programs/x86_64-linux/relion/2.1b1_cu8.0/bin/relion_refine_mpi(main+0x69)[0x40a3a9]
[bc-gpu1:05575] [ 7] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b64808a2c05]
[bc-gpu1:05575] [ 8] /programs/x86_64-linux/relion/2.1b1_cu8.0/bin/relion_refine_mpi[0x40a511]
[bc-gpu1:05575] *** End of error message ***
ERROR: unknown error in /programs/x86_64-linux/relion/2.1b1_cu8.0/src/gpu_utils/cuda_projector.cu at line 126 (error-code 30)
[bc-gpu1:05576] *** Process received signal ***
[bc-gpu1:05576] Signal: Segmentation fault (11)
[bc-gpu1:05576] Signal code: (-6)
[bc-gpu1:05576] Failing at address: 0x82ab000015c8
[bc-gpu1:05576] [ 0] /lib64/libpthread.so.0(+0xf5e0)[0x2b721ae745e0]
[bc-gpu1:05576] [ 1] /lib64/libpthread.so.0(raise+0x2b)[0x2b721ae744ab]
[bc-gpu1:05576] [ 2] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_gpu_util.so(_ZN13CudaProjector9setMdlDimEiiiiiii+0x5bb)[0x2b7219d1e20b]
[bc-gpu1:05576] [ 3] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_gpu_util.so(_ZN14MlDeviceBundle22setupFixedSizedObjectsEv+0x252)[0x2b7219d25c52]
[bc-gpu1:05576] [ 4] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_lib.so(_ZN14MlOptimiserMpi11expectationEv+0x118d)[0x2b720fef344d]
[bc-gpu1:05576] [ 5] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_lib.so(_ZN14MlOptimiserMpi7iterateEv+0x96)[0x2b720ff014f6]
[bc-gpu1:05576] [ 6] /programs/x86_64-linux/relion/2.1b1_cu8.0/bin/relion_refine_mpi(main+0x69)[0x40a3a9]
[bc-gpu1:05576] [ 7] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b721b0a2c05]
[bc-gpu1:05576] [ 8] /programs/x86_64-linux/relion/2.1b1_cu8.0/bin/relion_refine_mpi[0x40a511]
[bc-gpu1:05576] *** End of error message ***
ERROR: unknown error in /programs/x86_64-linux/relion/2.1b1_cu8.0/src/gpu_utils/cuda_projector.cu at line 126 (error-code 30)
[bc-gpu1:05577] *** Process received signal ***
[bc-gpu1:05577] Signal: Segmentation fault (11)
[bc-gpu1:05577] Signal code: (-6)
[bc-gpu1:05577] Failing at address: 0x82ab000015c9
[bc-gpu1:05577] [ 0] /lib64/libpthread.so.0(+0xf5e0)[0x2b631af855e0]
[bc-gpu1:05577] [ 1] /lib64/libpthread.so.0(raise+0x2b)[0x2b631af854ab]
[bc-gpu1:05577] [ 2] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_gpu_util.so(_ZN13CudaProjector9setMdlDimEiiiiiii+0x5bb)[0x2b6319e2f20b]
[bc-gpu1:05577] [ 3] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_gpu_util.so(_ZN14MlDeviceBundle22setupFixedSizedObjectsEv+0x252)[0x2b6319e36c52]
[bc-gpu1:05577] [ 4] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_lib.so(_ZN14MlOptimiserMpi11expectationEv+0x118d)[0x2b631000444d]
[bc-gpu1:05577] [ 5] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_lib.so(_ZN14MlOptimiserMpi7iterateEv+0x96)[0x2b63100124f6]
[bc-gpu1:05577] [ 6] /programs/x86_64-linux/relion/2.1b1_cu8.0/bin/relion_refine_mpi(main+0x69)[0x40a3a9]
[bc-gpu1:05577] [ 7] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b631b1b3c05]
[bc-gpu1:05577] [ 8] /programs/x86_64-linux/relion/2.1b1_cu8.0/bin/relion_refine_mpi[0x40a511]
[bc-gpu1:05577] *** End of error message ***
ERROR: unknown error in /programs/x86_64-linux/relion/2.1b1_cu8.0/src/gpu_utils/cuda_projector.cu at line 126 (error-code 30)
[bc-gpu1:05574] *** Process received signal ***
[bc-gpu1:05574] Signal: Segmentation fault (11)
[bc-gpu1:05574] Signal code: (-6)
[bc-gpu1:05574] Failing at address: 0x82ab000015c6
[bc-gpu1:05574] [ 0] /lib64/libpthread.so.0(+0xf5e0)[0x2aef95cfb5e0]
[bc-gpu1:05574] [ 1] /lib64/libpthread.so.0(raise+0x2b)[0x2aef95cfb4ab]
[bc-gpu1:05574] [ 2] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_gpu_util.so(_ZN13CudaProjector9setMdlDimEiiiiiii+0x5bb)[0x2aef94ba520b]
[bc-gpu1:05574] [ 3] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_gpu_util.so(_ZN14MlDeviceBundle22setupFixedSizedObjectsEv+0x252)[0x2aef94bacc52]
[bc-gpu1:05574] [ 4] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_lib.so(_ZN14MlOptimiserMpi11expectationEv+0x118d)[0x2aef8ad7a44d]
[bc-gpu1:05574] [ 5] /programs/x86_64-linux/relion/2.1b1_cu8.0/lib/librelion_lib.so(_ZN14MlOptimiserMpi7iterateEv+0x96)[0x2aef8ad884f6]
[bc-gpu1:05574] [ 6] /programs/x86_64-linux/relion/2.1b1_cu8.0/bin/relion_refine_mpi(main+0x69)[0x40a3a9]
[bc-gpu1:05574] [ 7] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2aef95f29c05]
[bc-gpu1:05574] [ 8] /programs/x86_64-linux/relion/2.1b1_cu8.0/bin/relion_refine_mpi[0x40a511]
[bc-gpu1:05574] *** End of error message ***
ERROR: unknown error in /programs/x86_64-linux/relion/2.1b1_cu8.0/src/gpu_utils/cuda_projector.cu at line 127 (error-code 30)
ERROR: unknown error in /programs/x86_64-linux/relion/2.1b1_cu8.0/src/gpu_utils/cuda_projector.cu at line 127 (error-code 30)

validate tomogram_ids against tilt image files during import

bforsbe added major bug labels Jan 26, 2017

biochem-fan closed this as completed Jun 27, 2020

scheres added a commit that referenced this issue Jul 23, 2024

Merge pull request #122 from ranganawarshamanage/validate_tomogram_ids

7d3e2ff

validate tomogram_ids against tilt image files during import

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relion_helix_toolbox doesn't work #122

relion_helix_toolbox doesn't work #122

bforsbe commented Oct 10, 2016

bforsbe commented Oct 12, 2016

bforsbe commented Oct 12, 2016

bforsbe commented Oct 12, 2016

bforsbe commented Oct 12, 2016

bforsbe commented Oct 13, 2016

bforsbe commented Oct 13, 2016

bforsbe commented Oct 13, 2016

bforsbe commented Oct 13, 2016

bforsbe commented Oct 13, 2016

bforsbe commented Oct 14, 2016

bforsbe commented Oct 14, 2016

bforsbe commented Oct 17, 2016

bforsbe commented Oct 17, 2016

bforsbe commented Oct 17, 2016

bforsbe commented Oct 18, 2016

bforsbe commented Oct 18, 2016

bforsbe commented Oct 18, 2016

bforsbe commented Oct 18, 2016

bforsbe commented Oct 18, 2016

bforsbe commented Oct 18, 2016

munanbt2004 commented Oct 31, 2017

relion_helix_toolbox doesn't work #122

relion_helix_toolbox doesn't work #122

Comments

bforsbe commented Oct 10, 2016

bforsbe commented Oct 12, 2016

bforsbe commented Oct 12, 2016

Only one option can be specified at one time! valid_options = 127 File: /scicore/pfs/mcleod/relion2-beta/src/apps/helix_toolbox.cpp line: 294

Only one option can be specified at one time! valid_options = 128 File: /scicore/pfs/mcleod/relion2-beta/src/apps/helix_toolbox.cpp line: 294

bforsbe commented Oct 12, 2016

bforsbe commented Oct 12, 2016

bforsbe commented Oct 13, 2016

bforsbe commented Oct 13, 2016

bforsbe commented Oct 13, 2016

bforsbe commented Oct 13, 2016

bforsbe commented Oct 13, 2016

bforsbe commented Oct 14, 2016

bforsbe commented Oct 14, 2016

bforsbe commented Oct 17, 2016

bforsbe commented Oct 17, 2016

[wangji@login11 fourth_round]$ relion_helix_toolbox --remove_bad_ctf --i run_data.star --o out.star --ctf_fom_min 0.1 --o out.star --EPA_lowest_res 4 Number of micrographs (input / output) = 6324 / 1772

bforsbe commented Oct 17, 2016

bforsbe commented Oct 18, 2016

bforsbe commented Oct 18, 2016

bforsbe commented Oct 18, 2016

bforsbe commented Oct 18, 2016

bforsbe commented Oct 18, 2016

bforsbe commented Oct 18, 2016

munanbt2004 commented Oct 31, 2017

Only one option can be specified at one time! valid_options = 127
File: /scicore/pfs/mcleod/relion2-beta/src/apps/helix_toolbox.cpp line: 294

Only one option can be specified at one time! valid_options = 128
File: /scicore/pfs/mcleod/relion2-beta/src/apps/helix_toolbox.cpp line: 294

[wangji@login11 fourth_round]$ relion_helix_toolbox --remove_bad_ctf --i run_data.star --o out.star --ctf_fom_min 0.1 --o out.star --EPA_lowest_res 4
Number of micrographs (input / output) = 6324 / 1772