Menu
▾
▴
scipion-users — Mailing list for Scipion users
You can subscribe to this list here.
| 2016 |
Jan
(2) |
Feb
(13) |
Mar
(9) |
Apr
(4) |
May
(5) |
Jun
(2) |
Jul
(8) |
Aug
(3) |
Sep
(25) |
Oct
(7) |
Nov
(49) |
Dec
(15) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2017 |
Jan
(24) |
Feb
(36) |
Mar
(53) |
Apr
(44) |
May
(37) |
Jun
(34) |
Jul
(12) |
Aug
(15) |
Sep
(14) |
Oct
(9) |
Nov
(9) |
Dec
(7) |
| 2018 |
Jan
(16) |
Feb
(9) |
Mar
(27) |
Apr
(39) |
May
(8) |
Jun
(24) |
Jul
(22) |
Aug
(11) |
Sep
(1) |
Oct
|
Nov
|
Dec
|
| 2019 |
Jan
(4) |
Feb
(5) |
Mar
|
Apr
(1) |
May
(21) |
Jun
(13) |
Jul
(31) |
Aug
(22) |
Sep
(9) |
Oct
(19) |
Nov
(24) |
Dec
(12) |
| 2020 |
Jan
(30) |
Feb
(12) |
Mar
(16) |
Apr
(4) |
May
(37) |
Jun
(17) |
Jul
(19) |
Aug
(15) |
Sep
(26) |
Oct
(84) |
Nov
(64) |
Dec
(55) |
| 2021 |
Jan
(18) |
Feb
(58) |
Mar
(26) |
Apr
(88) |
May
(51) |
Jun
(36) |
Jul
(31) |
Aug
(37) |
Sep
(79) |
Oct
(15) |
Nov
(29) |
Dec
(8) |
| 2022 |
Jan
(5) |
Feb
(8) |
Mar
(29) |
Apr
(21) |
May
(11) |
Jun
(11) |
Jul
(18) |
Aug
(16) |
Sep
(6) |
Oct
(10) |
Nov
(23) |
Dec
(1) |
| 2023 |
Jan
(18) |
Feb
|
Mar
(4) |
Apr
|
May
(3) |
Jun
(10) |
Jul
(1) |
Aug
|
Sep
|
Oct
(1) |
Nov
(3) |
Dec
(5) |
| 2024 |
Jan
(2) |
Feb
|
Mar
|
Apr
|
May
|
Jun
(1) |
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2025 |
Jan
(1) |
Feb
|
Mar
|
Apr
(5) |
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: Pablo C. <pc...@cn...> - 2022-02-16 09:24:52
|
Hi Christian! I see now your needs. You can certainly remove files in extra folders to free space. Rerun is an option, but for consistency, if you rerun a protocol with "hanging protocols", they will be rerun to. Probably, the best approach, is to make a copy and run the copy. Regarding repeatability....there are some methods that are not deterministic, so for those you will not get exactly the same results after a rerun. But there is no workaround here, we need to live with it. Since Scipion is extensible, there is the option to create your own plugin with an archival protocol following your rules, that, even could break the "imposed consistency" and do what you need, but for this you will need some python programing skills and some guidance you can count on with. On 16/2/22 9:29, Christian Tüting wrote: > Hi Pablo, > > thank your for your anwser and sorry for the late response. > > I have a followed up question on point (a). I think, this is obvious > that you shouldn't delete any extracted particles or motioncorrected > images *during* the analysis. > > > But let me explain our current situation. > > We have couple of finished project, done in Scipion. So we would like to > archive the projects, so if someone had any questions, or we need to > continue the analysis (e.g. for revisions etc.), they should be easily > recoverable. > Sure, we can go and save the entire project folder, but this is in my > opinion not needed. > This is because, we have to store the original raw data for 10 years. > Thereby, for example, extracted particles are just a redundant > information, as one only needs (a) the micrograph (or the motion > corrected) and (b) the particle coordinates. > > So my question is, could I delete the extracted particles and/or the > motion correction by deleting everything in the "extra" folder in the > corresponding job, but recreate the exact same information by just > re-run the job in scipion? > > Or is re-running the job creating different files, e.g. because a random > seed is used? And all related jobs will fail, as they do not find the > correct files? > > Thanks in Advance > > Christian > > ps. not sure if this mail is now send twice, I got the error that my > first mail was terminated: > > Transcript of session follows: > Command: MAIL FROM:<chr...@bi...> > Response: 550 sender address not allowed > > >>>> Pablo Conesa<pc...@cn...> 02/08/22 3:40 PM >>> > Hi Chistian, please see my thoughts in line. > > On 8/2/22 14:43, Christian Tüting wrote: >> Hi Scipion Team, >> >> I have a few questions regarding project cleaning and space usage. >> >> (a) "clean" the data of a job, but keep the settings. >> This is mainly for particle extraction jobs. These are often the jobs, > that requires the most space, but the job in principle could be redo at > any time, as you just need coordinates and box-size. In cryoSPARC, one > can easily clean a job by "Clear Job", which deletes all the generated > files, but keep the settings. Is something similar possible in scipion > as well? > > Scipion protocols are often designed to save space. It is true that > particle extraction is a step where "new images are generated" but, > unless later on, you apply some "filtering/crop/resize" operations > (these also are those kind generating new images), the new images > should be reuse. > > It is true that we can clean them, but then nothing after this will > work. All refinements, 2d classification etc should point to the same > stacks produced at the extraction step. > >> (b) identify redundant and obsolete jobs. >> >> Often multiple rounds of picking, extracting and 2D classification are > done to get a good subset of particles. But the initial jobs, useful in > the beginning, are often not needed for the later refinements. Is there > a way of identifying jobs, that are potentially obsolete? Again, > deleting them would be over the top, but cleaning these data as > questioned in (a). Also, if a project is challenging, one might run > multiple parallel jobs eventually creating redundancy, which blocks also > space. Is there a easy way of analysing the workflow tree? I saw that > there are some sqlite databases in the project folders, but it was not > clear for me, how I can extract the tree from there, to see, if there > are multiple/redundant jobs. > We haven't done that effort, but you could select one protocol (let's > say a final one with nice results), right click on it and "select to > here"....protocols not selected didn't contribute to the final result > and may be deleted. You could also identify a "dead branch" and delete > that branch. If your project is one of those I've seen with several > hundreds of protocols I can see this is more complicated. >> (c) Identify dead-end forks. >> This goes hand-in-hand with (b). Is there a easy way of getting the > entire tree from the project folder/database, to analyse it > indecode, to get the information, without using the scipion gui (which is a > bit laggy over ssh and x-forwarding). > Scipion, has a strong almost 100% complete API. I'd say is possible but > not trivial. Depends on your programming skills. We usually connect > though a vnc server, but may be this is not possible in your case. >> Best >> Christian >> >> >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Grigory S. <sha...@gm...> - 2022-02-14 13:30:32
|
Hi Adria, Could you please create an issue <https://github.com/scipion-em/scipion-em-relion/issues/new?assignees=&labels=&template=bug_report.md&title=> for this? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, Feb 14, 2022 at 1:26 PM Adria Alcaide Jimenez <aa...@ib...> wrote: > Hello Scipion team, > > I have a question regarding Relion extract particles. > > When I do a first particle picking (xmipp) and I extract the particles I > have no problem but > when I get 2D classes with Relion and I perform an autopicking with Relion > and the 2D reference averages, I can not extract the particles with Relion > extract particles. > > The error that appears is : "local variable 'posSet' referenced before > assignment". > > I have tried to extract particles with Xmipp and I can, but then when I > perform the 2D classification with Relion 2D class it appears the same > error. I don't know what does it mean or how can I solve it. > > Do you have any idea? > > Thank you in advance for your help, > > Adrià. > > -- > Adrià Alcaide i Jiménez > *PhD student* > Structural Biology Unit (SBU) > Consejo Superior de Investigaciones Científicas (CSIC) > Instituto de Biología Molecular de Barcelona (IBMB) > C/Baldiri i Reixac 10-12 Edifici Cluster > 08028 Barcelona (Spain) > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Adria A. J. <aa...@ib...> - 2022-02-14 13:25:53
|
Hello Scipion team, I have a question regarding Relion extract particles. When I do a first particle picking (xmipp) and I extract the particles I have no problem but when I get 2D classes with Relion and I perform an autopicking with Relion and the 2D reference averages, I can not extract the particles with Relion extract particles. The error that appears is : "local variable 'posSet' referenced before assignment". I have tried to extract particles with Xmipp and I can, but then when I perform the 2D classification with Relion 2D class it appears the same error. I don't know what does it mean or how can I solve it. Do you have any idea? Thank you in advance for your help, Adrià. -- Adrià Alcaide i Jiménez *PhD student* Structural Biology Unit (SBU) Consejo Superior de Investigaciones Científicas (CSIC) Instituto de Biología Molecular de Barcelona (IBMB) C/Baldiri i Reixac 10-12 Edifici Cluster 08028 Barcelona (Spain) |
|
From: Pablo C. <pc...@cn...> - 2022-02-08 14:39:38
|
Hi Chistian, please see my thoughts in line. On 8/2/22 14:43, Christian Tüting wrote: > Hi Scipion Team, > > I have a few questions regarding project cleaning and space usage. > > (a) "clean" the data of a job, but keep the settings. > This is mainly for particle extraction jobs. These are often the jobs, that requires the most space, but the job in principle could be redo at any time, as you just need coordinates and box-size. In cryoSPARC, one can easily clean a job by "Clear Job", which deletes all the generated files, but keep the settings. Is something similar possible in scipion as well? Scipion protocols are often designed to save space. It is true that particle extraction is a step where "new images are generated" but, unless later on, you apply some "filtering/crop/resize" operations (these also are those kind generating new images), the new images should be reuse. It is true that we can clean them, but then nothing after this will work. All refinements, 2d classification etc should point to the same stacks produced at the extraction step. > > (b) identify redundant and obsolete jobs. > > Often multiple rounds of picking, extracting and 2D classification are done to get a good subset of particles. But the initial jobs, useful in the beginning, are often not needed for the later refinements. Is there a way of identifying jobs, that are potentially obsolete? Again, deleting them would be over the top, but cleaning these data as questioned in (a). Also, if a project is challenging, one might run multiple parallel jobs eventually creating redundancy, which blocks also space. Is there a easy way of analysing the workflow tree? I saw that there are some sqlite databases in the project folders, but it was not clear for me, how I can extract the tree from there, to see, if there are multiple/redundant jobs. We haven't done that effort, but you could select one protocol (let's say a final one with nice results), right click on it and "select to here"....protocols not selected didn't contribute to the final result and may be deleted. You could also identify a "dead branch" and delete that branch. If your project is one of those I've seen with several hundreds of protocols I can see this is more complicated. > > (c) Identify dead-end forks. > This goes hand-in-hand with (b). Is there a easy way of getting the entire tree from the project folder/database, to analyse it independently? Like getting the node information and use some python code, to get the information, without using the scipion gui (which is a bit laggy over ssh and x-forwarding). Scipion, has a strong almost 100% complete API. I'd say is possible but not trivial. Depends on your programming skills. We usually connect though a vnc server, but may be this is not possible in your case. > > Best > Christian > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Christian T. <chr...@bi...> - 2022-02-08 13:58:26
|
Hi Scipion Team, I have a few questions regarding project cleaning and space usage. (a) "clean" the data of a job, but keep the settings. This is mainly for particle extraction jobs. These are often the jobs, that requires the most space, but the job in principle could be redo at any time, as you just need coordinates and box-size. In cryoSPARC, one can easily clean a job by "Clear Job", which deletes all the generated files, but keep the settings. Is something similar possible in scipion as well? (b) identify redundant and obsolete jobs. Often multiple rounds of picking, extracting and 2D classification are done to get a good subset of particles. But the initial jobs, useful in the beginning, are often not needed for the later refinements. Is there a way of identifying jobs, that are potentially obsolete? Again, deleting them would be over the top, but cleaning these data as questioned in (a). Also, if a project is challenging, one might run multiple parallel jobs eventually creating redundancy, which blocks also space. Is there a easy way of analysing the workflow tree? I saw that there are some sqlite databases in the project folders, but it was not clear for me, how I can extract the tree from there, to see, if there are multiple/redundant jobs. (c) Identify dead-end forks. This goes hand-in-hand with (b). Is there a easy way of getting the entire tree from the project folder/database, to analyse it independently? Like getting the node information and use some python code, to get the information, without using the scipion gui (which is a bit laggy over ssh and x-forwarding). Best Christian |
|
From: Roberto M. <ro...@cn...> - 2022-02-04 22:01:14
|
Hi,
Since the error is:
ERROR:
Allocate: No space left
I guess you do not have enough memory in your computer.
cheers
Roberto
On Fri, Feb 4, 2022 at 7:40 PM Bing Wang via scipion-users <
sci...@li...> wrote:
> Hi there,
>
> Does anyone test the tutorial of localized reconstruction in scipion and
> know the causes of the error below (i.e. panel of Output Log)?
> The running is based on the online guide of localized reconstruction in
> Scipion. The error comes out when I was running "Protocol: relion -
> substract projection" to substract hexons signal from virus particles. The
> error output log shows that the failed command is relion_project. Then I
> copied the command and run again, and it showed detailed error as below
> (i.e. panel of relion_project_error_message). Thanks a lot in advance for
> the answer!
>
> ###################Output Log###########################
> 00001: Logging configured. STDOUT -->
> Runs/001428_ProtRelionSubtract/logs/run.stdout , STDERR -->
> Runs/001428_ProtRelionSubtract/logs/run.stderr
> 00002: RUNNING PROTOCOL -----------------
> 00003: Protocol starts
> 00004: Hostname: pagoda.biophysics.fsu.edu
> 00005: PID: 47092
> 00006: pyworkflow: 3.0.18
> 00007: plugin: relion
> 00008: plugin v: 4.0b8
> 00009: currentDir:
> /data1/bwang/cryoem/ScipionUserData/projects/HAdV-TFibre-Tutorial
> 00010: workingDir: Runs/001428_ProtRelionSubtract
> 00011: runMode: Continue
> 00012: MPI: 1
> 00013: threads: 1
> 00014: Starting at step: 1
> 00015: Running steps
> 00016: STARTED: convertInputStep, step 1, time 2022-01-24 16:33:59.856460
> 00017: convertBinaryFiles: creating soft links.
> 00018: Root: Runs/001428_ProtRelionSubtract/extra/input ->
> Runs/000002_ProtImportParticles/extra
> 00019: FINISHED: convertInputStep, step 1, time 2022-01-24
> 16:34:00.831167
> 00020: STARTED: subtractStep, step 2, time 2022-01-24 16:34:00.914606
> 00021: 000/??? sec ~~(,_,">
> [oo]
> 00022: 49/ 49 sec
> ............................................................~~(,_,">
> 00023: 000/??? sec ~~(,_,">
> [oo]Logging configured. STDOUT -->
> Runs/001428_ProtRelionSubtract/logs/run.stdout , STDERR -->
> Runs/001428_ProtRelionSubtract/logs/run.stderr
> 00024: RUNNING PROTOCOL -----------------
> 00025: Protocol starts
> 00026: Hostname: pagoda.biophysics.fsu.edu
> 00027: PID: 55418
> 00028: pyworkflow: 3.0.18
> 00029: plugin: relion
> 00030: plugin v: 4.0b8
> 00031: currentDir:
> /data1/bwang/cryoem/ScipionUserData/projects/HAdV-TFibre-Tutorial
> 00032: workingDir: Runs/001428_ProtRelionSubtract
> 00033: runMode: Continue
> 00034: MPI: 1
> 00035: threads: 1
> 00036: Starting at step: 2
> 00037: Running steps
> 00038: STARTED: subtractStep, step 2, time 2022-01-24 16:37:48.994518
> 00039: 000/??? sec ~~(,_,">
> [oo]
> 00040: 46/ 46 sec
> ............................................................~~(,_,">
> 00041: 000/??? sec ~~(,_,">
> [oo]
> 00042: 50/ 50 sec
> ............................................................~~(,_,">
> 00043: ** Running command: relion_image_handler --i
> Runs/001382_ProtRelionCreateMask3D/extra/mask.mrc --o
> Runs/001428_ProtRelionSubtract/tmp/mask.mrc --angpix 1.31000
> --multiply_constant -1
> 00044: ** Running command: relion_image_handler --i
> Runs/001428_ProtRelionSubtract/tmp/mask.mrc --o
> Runs/001428_ProtRelionSubtract/tmp/mask.mrc --angpix 1.31000
> --threshold_above 1 --threshold_below 0 --add_constant 1
> 00045: relion_project --i
> Runs/001428_ProtRelionSubtract/extra/import_emd_11008.mrc --subtract_exp
> --angpix 1.310 --mask Runs/001428_ProtRelionSubtract/tmp/mask.mrc --ctf
> --ang Runs/001428_ProtRelionSubtract/extra/input_particles.star --o
> Runs/001428_ProtRelionSubtract/extra/particles_subtracted
> 00046: Reading map:
> Runs/001428_ProtRelionSubtract/extra/import_emd_11008.mrc
> 00047: Done reading map!
> 00048: Reading STAR file with all angles
> Runs/001428_ProtRelionSubtract/extra/input_particles.star
> 00049: Done reading STAR file!
> 00050: Protocol failed: Command ' relion_project --i
> Runs/001428_ProtRelionSubtract/extra/import_emd_11008.mrc --subtract_exp
> --angpix 1.310 --mask Runs/001428_ProtRelionSubtract/tmp/mask.mrc --ctf
> --ang Runs/001428_ProtRelionSubtract/extra/input_particles.star --o
> Runs/001428_ProtRelionSubtract/extra/particles_subtracted' returned
> non-zero exit status 1.
> 00051: FAILED: subtractStep, step 2, time 2022-01-24 16:40:57.727689
> ###################Output Log###########################
>
>
>
>
>
>
> ########################
> relion_project_error_message#########################
> bwang@pagoda$ relion_project --i
> Runs/001428_ProtRelionSubtract/extra/import_emd_11008.mrc --subtract_exp
> --angpix 1.310 --mask Runs/001428_ProtRelionSubtract/tmp/mask.mrc --ctf
> --ang Runs/001428_ProtRelionSubtract/extra/input_particles.star --o
> Runs/001428_ProtRelionSubtract/extra/particles_subtracted
> Reading map: Runs/001428_ProtRelionSubtract/extra/import_emd_11008.mrc
> Done reading map!
> Reading STAR file with all angles
> Runs/001428_ProtRelionSubtract/extra/input_particles.star
> Done reading STAR file!
> in:
> /data2/bwang/Downloads/relion_build/relion_gpu/relion/src/multidim_array.h,
> line 702
> ERROR:
> Allocate: No space left
> === Backtrace ===
> relion_project(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x6d)
> [0x47aedd]
> relion_project(_ZN13MultidimArrayIdE12coreAllocateEv+0x351) [0x445321]
> relion_project(_ZN13MultidimArrayIdE9initZerosEllll+0xc2) [0x477ef2]
> relion_project(_ZN9Projector26computeFourierTransformMapER13MultidimArrayIdES2_iibbiPKS1_b+0x293)
> [0x473423]
> relion_project(_ZN18project_parameters7projectEv+0x1c93) [0x4553a3]
> relion_project(main+0x49) [0x43ae69]
> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7fb5c1614840]
> relion_project(_start+0x29) [0x43db89]
> ==================
> ERROR:
> Allocate: No space left
> ########################
> relion_project_error_message#########################
>
>
>
> Best,
> Bing
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Bing W. <bw...@fs...> - 2022-02-04 18:40:22
|
Hi there, Does anyone test the tutorial of localized reconstruction in scipion and know the causes of the error below (i.e. panel of Output Log)? The running is based on the online guide of localized reconstruction in Scipion. The error comes out when I was running "Protocol: relion - substract projection" to substract hexons signal from virus particles. The error output log shows that the failed command is relion_project. Then I copied the command and run again, and it showed detailed error as below (i.e. panel of relion_project_error_message). Thanks a lot in advance for the answer! ###################Output Log########################### 00001: Logging configured. STDOUT --> Runs/001428_ProtRelionSubtract/logs/run.stdout , STDERR --> Runs/001428_ProtRelionSubtract/logs/run.stderr 00002: RUNNING PROTOCOL ----------------- 00003: Protocol starts 00004: Hostname: pagoda.biophysics.fsu.edu 00005: PID: 47092 00006: pyworkflow: 3.0.18 00007: plugin: relion 00008: plugin v: 4.0b8 00009: currentDir: /data1/bwang/cryoem/ScipionUserData/projects/HAdV-TFibre-Tutorial 00010: workingDir: Runs/001428_ProtRelionSubtract 00011: runMode: Continue 00012: MPI: 1 00013: threads: 1 00014: Starting at step: 1 00015: Running steps 00016: STARTED: convertInputStep, step 1, time 2022-01-24 16:33:59.856460 00017: convertBinaryFiles: creating soft links. 00018: Root: Runs/001428_ProtRelionSubtract/extra/input -> Runs/000002_ProtImportParticles/extra 00019: FINISHED: convertInputStep, step 1, time 2022-01-24 16:34:00.831167 00020: STARTED: subtractStep, step 2, time 2022-01-24 16:34:00.914606 00021: 000/??? sec ~~(,_,"> [oo] 00022: 49/ 49 sec ............................................................~~(,_,"> 00023: 000/??? sec ~~(,_,"> [oo]Logging configured. STDOUT --> Runs/001428_ProtRelionSubtract/logs/run.stdout , STDERR --> Runs/001428_ProtRelionSubtract/logs/run.stderr 00024: RUNNING PROTOCOL ----------------- 00025: Protocol starts 00026: Hostname: pagoda.biophysics.fsu.edu 00027: PID: 55418 00028: pyworkflow: 3.0.18 00029: plugin: relion 00030: plugin v: 4.0b8 00031: currentDir: /data1/bwang/cryoem/ScipionUserData/projects/HAdV-TFibre-Tutorial 00032: workingDir: Runs/001428_ProtRelionSubtract 00033: runMode: Continue 00034: MPI: 1 00035: threads: 1 00036: Starting at step: 2 00037: Running steps 00038: STARTED: subtractStep, step 2, time 2022-01-24 16:37:48.994518 00039: 000/??? sec ~~(,_,"> [oo] 00040: 46/ 46 sec ............................................................~~(,_,"> 00041: 000/??? sec ~~(,_,"> [oo] 00042: 50/ 50 sec ............................................................~~(,_,"> 00043: ** Running command: relion_image_handler --i Runs/001382_ProtRelionCreateMask3D/extra/mask.mrc --o Runs/001428_ProtRelionSubtract/tmp/mask.mrc --angpix 1.31000 --multiply_constant -1 00044: ** Running command: relion_image_handler --i Runs/001428_ProtRelionSubtract/tmp/mask.mrc --o Runs/001428_ProtRelionSubtract/tmp/mask.mrc --angpix 1.31000 --threshold_above 1 --threshold_below 0 --add_constant 1 00045: relion_project --i Runs/001428_ProtRelionSubtract/extra/import_emd_11008.mrc --subtract_exp --angpix 1.310 --mask Runs/001428_ProtRelionSubtract/tmp/mask.mrc --ctf --ang Runs/001428_ProtRelionSubtract/extra/input_particles.star --o Runs/001428_ProtRelionSubtract/extra/particles_subtracted 00046: Reading map: Runs/001428_ProtRelionSubtract/extra/import_emd_11008.mrc 00047: Done reading map! 00048: Reading STAR file with all angles Runs/001428_ProtRelionSubtract/extra/input_particles.star 00049: Done reading STAR file! 00050: Protocol failed: Command ' relion_project --i Runs/001428_ProtRelionSubtract/extra/import_emd_11008.mrc --subtract_exp --angpix 1.310 --mask Runs/001428_ProtRelionSubtract/tmp/mask.mrc --ctf --ang Runs/001428_ProtRelionSubtract/extra/input_particles.star --o Runs/001428_ProtRelionSubtract/extra/particles_subtracted' returned non-zero exit status 1. 00051: FAILED: subtractStep, step 2, time 2022-01-24 16:40:57.727689 ###################Output Log########################### ######################## relion_project_error_message######################### bwang@pagoda$ relion_project --i Runs/001428_ProtRelionSubtract/extra/import_emd_11008.mrc --subtract_exp --angpix 1.310 --mask Runs/001428_ProtRelionSubtract/tmp/mask.mrc --ctf --ang Runs/001428_ProtRelionSubtract/extra/input_particles.star --o Runs/001428_ProtRelionSubtract/extra/particles_subtracted Reading map: Runs/001428_ProtRelionSubtract/extra/import_emd_11008.mrc Done reading map! Reading STAR file with all angles Runs/001428_ProtRelionSubtract/extra/input_particles.star Done reading STAR file! in: /data2/bwang/Downloads/relion_build/relion_gpu/relion/src/multidim_array.h, line 702 ERROR: Allocate: No space left === Backtrace === relion_project(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x6d) [0x47aedd] relion_project(_ZN13MultidimArrayIdE12coreAllocateEv+0x351) [0x445321] relion_project(_ZN13MultidimArrayIdE9initZerosEllll+0xc2) [0x477ef2] relion_project(_ZN9Projector26computeFourierTransformMapER13MultidimArrayIdES2_iibbiPKS1_b+0x293) [0x473423] relion_project(_ZN18project_parameters7projectEv+0x1c93) [0x4553a3] relion_project(main+0x49) [0x43ae69] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7fb5c1614840] relion_project(_start+0x29) [0x43db89] ================== ERROR: Allocate: No space left ######################## relion_project_error_message######################### Best, Bing |
|
From: Alberto G. M. <alb...@cn...> - 2022-01-25 06:17:28
|
Dear all, XMIPP-Team have prepared the new version of Xmipp. Please welcome to *Xmipp 3.22.01-Eris * The main new features are this*.* <https://github.com/I2PC/xmipp/blob/devel/CHANGELOG.md>**Feel free toinstall it <https://github.com/I2PC/xmipp#standalone-installation>, test it, report any problems <https://github.com/I2PC/xmipp/issues> if they arise and above all enjoy it! Best Regards Xmipp-Team |
|
From: Yunior C. F. R. <cfo...@cn...> - 2022-01-20 10:54:17
|
Hi all, I have made a new release of the cryosparc plugin(v3.3.3). A new 3D reconstruction protocol has been added as well as an improvement in the performance of all the protocols to generate the outputs, which in many cases took longer than the processing itself. Any problem please let me know. Best Regards Scipion Team |
|
From: Grigory S. <sha...@gm...> - 2022-01-17 19:02:23
|
Hi, Though I dont use relion picker, I believe it works well only without MPIs. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, Jan 17, 2022 at 6:45 PM Pablo Conesa <pc...@cn...> wrote: > Hi Maria! > > It may be either: > > 1. Installation error > > 2. data related problem > > 3. a bug > > > To discard 1, quite often is useful to run a related test > > For this, if you run: scipion3 tests --grep relion. > > You'll get lots of tests that relion plugin maintainer regularly run to > ensure new changes does not break the functionality: > > scipion3 tests relion.tests.test_workflow_relion3 > scipion3 tests > relion.tests.test_workflow_relion3.TestWorkflowRelion3Betagal > scipion3 tests relion.tests.test_protocols_relion3 > scipion3 tests > relion.tests.test_protocols_relion3.TestRelion31ImportParticles > scipion3 tests relion.tests.test_protocols_relion3.Relion3TestMultiBody > scipion3 tests relion.tests.test_protocols_relion3.Relion3TestMotioncor > scipion3 tests > relion.tests.test_protocols_relion3.Relion3TestAssignOptics > scipion3 tests relion.tests.test_protocols_relion > scipion3 tests > relion.tests.test_protocols_relion.TestRelionSymmetrizeVolume > scipion3 tests relion.tests.test_protocols_relion.TestRelionSubtract > scipion3 tests relion.tests.test_protocols_relion.TestRelionResizeVolume > scipion3 tests > relion.tests.test_protocols_relion.TestRelionRemovePrefViews > scipion3 tests relion.tests.test_protocols_relion.TestRelionRefine > scipion3 tests relion.tests.test_protocols_relion.TestRelionPreprocess > scipion3 tests relion.tests.test_protocols_relion.TestRelionPostprocess > scipion3 tests relion.tests.test_protocols_relion.TestRelionPicking > scipion3 tests relion.tests.test_protocols_relion.TestRelionLocalRes > scipion3 tests relion.tests.test_protocols_relion.TestRelionInitialModel > scipion3 tests > relion.tests.test_protocols_relion.TestRelionExtractParticles > scipion3 tests > relion.tests.test_protocols_relion.TestRelionExportParticles > scipion3 tests relion.tests.test_protocols_relion.TestRelionExportCtf > scipion3 tests > relion.tests.test_protocols_relion.TestRelionExpandSymmetry > scipion3 tests relion.tests.test_protocols_relion.TestRelionCreate3dMask > scipion3 tests relion.tests.test_protocols_relion.TestRelionClassify3D > scipion3 tests relion.tests.test_protocols_relion.TestRelionClassify2D > scipion3 tests > relion.tests.test_protocols_relion.TestRelionCenterAverages > scipion3 tests relion.tests.test_projection_subtraction_no_relion > scipion3 tests > relion.tests.test_projection_subtraction_no_relion.TestSubtractionProjection > scipion3 tests relion.tests.test_convert_relion > scipion3 tests relion.tests.test_convert_relion.TestRelionWriter > scipion3 tests relion.tests.test_convert_relion.TestRelionReader > scipion3 tests relion.tests.test_convert_relion.TestRelionOpticsGroups > scipion3 tests relion.tests.test_convert_relion.TestReconstruct > scipion3 tests relion.tests.test_convert_relion.TestConvertBinaryFiles > scipion3 tests relion.tests.test_convert_relion.TestAlignment > > > I'd choose --> scipion3 tests > relion.tests.test_protocols_relion.TestRelionPicking > > To verify it works. If so, then we discard point 1. > > > On 17/1/22 14:46, Anastasina, Maria wrote: > > Dear colleagues, > > Relion auto-picking jobs within Scipion 3.0.8 fail with the error message > pasted below. I am picking particles using 2D averages as references. These > averages come from a different dataset than the micrographs, and have been > re-scaled to match the pixel size using crop/resize protocol in Scipion. > > I don’t understand what exactly is going wrong and would be very > appreciative if any of you could suggest the reason for failure. > > Best regards, > Maria > > > 00001: RUNNING PROTOCOL ----------------- > 00002: Hostname: r15g05.bullx > 00003: PID: 135115 > 00004: pyworkflow: 3.0.16 > 00005: plugin: relion > 00006: plugin v: 3.1.1 > 00007: currentDir: > /scratch/project_2004278/ScipionUserData/projects/immTBEV > 00008: workingDir: Runs/025798_ProtRelion2Autopick > 00009: runMode: Continue > 00010: MPI: 4 > 00011: threads: 1 > 00012: Starting at step: 1 > 00013: Running steps > 00014: STARTED: convertInputStep, step 1, time 2022-01-17 15:15:42.193627 > 00015: FINISHED: convertInputStep, step 1, time 2022-01-17 > 15:15:42.565530 > 00016: STARTED: pickMicrographStep, step 2, time 2022-01-17 > 15:15:42.591236 > 00017: Picking micrograph: > Runs/000799_ProtMotionCorr/extra/GridSquare_29251179_Data_FoilHole_30265827_Data_29254225_29254227_20210330_060030_fractions_aligned_mic_DW.mrc > 00018: Some paths do not exist in: /usr/local/cuda/lib64 > 00019: srun `which relion_autopick_mpi` --pickname autopick --odir > "./" --particle_diameter 666 --angpix 1.10410 --shrink 0.000 --gpu "" --ref > /scratch/project_2004278/ScipionUserData/projects/immTBEV/Runs/025798_ProtRelion2Autopick/reference_2d.stk > --angpix_ref 1.10000 --invert --ang 5 --lowpass 20 --i > input_micrographs.star --threshold 0.250 --min_distance -1.000 > --max_stddev_noise 1.100 --min_avg_noise -999.000 > 00020: RELION version: 3.1.1 > 00021: Precision: BASE=double, CUDA-ACC=single > 00022: > 00023: === RELION MPI setup === > 00024: + Number of MPI processes = 5 > 00025: + Master (0) runs on host = r15g05.bullx > 00026: ================= > 00027: + Slave 1 runs on host = r15g05.bullx > 00028: + Slave 2 runs on host = r15g05.bullx > 00029: + Slave 3 runs on host = r15g05.bullx > 00030: + Slave 4 runs on host = r15g05.bullx > 00031: + Run autopicking on the following micrographs: > 00032: * mic_000007.mrc > 00033: WARNING!!! Pixel size in reference image header= 0 but you have > provided --angpix_ref 1.1 > 00034: + WARNING: Requested rescale of micrographs is 636 pixels. The > largest prime factor in FFTs is 53 > 00035: + WARNING: Will change rescaling of micrographs to 638 pixels, > because the prime factor then becomes 29 > 00036: + WARNING: add --skip_optimise_scale to your autopick command to > prevent rescaling > 00037: Initialising FFTs for the references and masks ... > 00038: 000/??? sec ~~(,_,"> > [oo] > 00039: 2/ 2 sec > ............................................................~~(,_,"> > 00040: + Using GPU device: 0 on MPI node: 0 > 00041: + Using GPU device: 1 on MPI node: 1 > 00042: + Using GPU device: 2 on MPI node: 2 > 00043: + Using GPU device: 3 on MPI node: 3 > 00044: + Using GPU device: 0 on MPI node: 4 > 00045: Autopicking ... > 00046: 000/??? sec ~~(,_,"> > [oo] > 00047: 6/ 6 sec > ............................................................~~(,_,"> > 00048: Generating logfile.pdf ... > 00049: 000/??? sec ~~(,_,"> > [oo] > 00050: 0/ 0 sec > ............................................................~~(,_,"> > 00051: Total number of particles from 1 micrographs is 0 > 00052: i.e. on average there were 0 particles per micrograph > 00053: terminate called after throwing an instance of 'std::bad_alloc' > 00054: what(): std::bad_alloc > 00055: [r15g05:135359] *** Process received signal *** > 00056: [r15g05:135359] Signal: Aborted (6) > 00057: [r15g05:135359] Signal code: (-6) > 00058: [r15g05:135359] [ 0] > /lib64/libpthread.so.0(+0xf630)[0x7f0aad9e5630] > 00059: [r15g05:135359] [ 1] > /lib64/libc.so.6(gsignal+0x37)[0x7f0aa8d15387] > 00060: [r15g05:135359] [ 2] /lib64/libc.so.6(abort+0x148)[0x7f0aa8d16a78] > 00061: [r15g05:135359] [ 3] > /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x94983)[0x7f0aa9443983] > 00062: [r15g05:135359] [ 4] > /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x9aaf6)[0x7f0aa9449af6] > 00063: [r15g05:135359] [ 5] > /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x9ab31)[0x7f0aa9449b31] > 00064: [r15g05:135359] [ 6] > /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x9ad63)[0x7f0aa9449d63] > 00065: [r15g05:135359] [ 7] > /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x9b22c)[0x7f0aa944a22c] > 00066: [r15g05:135359] [ 8] > /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_+0x57)[0x7f0ab6c64b87] > 00067: [r15g05:135359] [ 9] > /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZN7CPlot2D23ComputeLabelTickSpacingEddPdS0_S0_iNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x315)[0x7f0ab6c626b5] > 00068: [r15g05:135359] [10] > /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZN7CPlot2D20PrecomputeDimensionsEv+0x489)[0x7f0ab6c62eb9] > 00069: [r15g05:135359] [11] > /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZN7CPlot2D20OutputPostScriptPlotENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x51)[0x7f0ab6c63441] > 00070: [r15g05:135359] [12] > /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZN10AutoPicker18generatePDFLogfileEv+0x762)[0x7f0ab6c849a2] > 00071: [r15g05:135359] [13] > /appl/soft/math/scipion/3.0.7/software/em/relion-3.1.0/bin/relion_autopick_mpi(main+0x11c)[0x4024ec] > 00072: [r15g05:135359] [14] > /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f0aa8d01555] > 00073: [r15g05:135359] [15] > /appl/soft/math/scipion/3.0.7/software/em/relion-3.1.0/bin/relion_autopick_mpi[0x4025dc] > 00074: [r15g05:135359] *** End of error message *** > 00075: srun: error: r15g05: task 0: Aborted > 00076: srun: launch/slurm: _step_signal: Terminating StepId=10234377.0 > 00077: slurmstepd: error: *** STEP 10234377.0 ON r15g05 CANCELLED AT > 2022-01-17T15:25:37 *** > 00078: srun: error: r15g05: tasks 1-4: Terminated > 00079: srun: Force Terminated StepId=10234377.0 > 00080: Traceback (most recent call last): > 00081: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 197, in run > 00082: self._run() > 00083: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 248, in _run > 00084: resultFiles = self._runFunc() > 00085: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 244, in _runFunc > 00086: return self._func(*self._args) > 00087: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_particles_picking.py", > line 241, in pickMicrographStep > 00088: self._pickMicrograph(mic, *args) > 00089: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/relion/protocols/protocol_autopick.py", > line 44, in _pickMicrograph > 00090: self._pickMicrographList([mic], *args) > 00091: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/relion/protocols/protocol_autopick.py", > line 54, in _pickMicrographList > 00092: self._pickMicrographsFromStar(micStar, micsDir, *args) > 00093: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/relion/protocols/protocol_autopick_ref.py", > line 401, in _pickMicrographsFromStar > 00094: self.runJob(program, params, cwd=cwd) > 00095: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 1389, in runJob > 00096: self._stepsExecutor.runJob(self._log, program, arguments, > **kwargs) > 00097: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", > line 65, in runJob > 00098: process.runJob(log, programName, params, > 00099: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 52, in runJob > 00100: return runCommand(command, env, cwd) > 00101: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 67, in runCommand > 00102: check_call(command, shell=True, stdout=sys.stdout, > stderr=sys.stderr, > 00103: File > "/appl/soft/math/scipion/3.8.7-gnu8.3.0/lib/python3.8/subprocess.py", line > 364, in check_call > 00104: raise CalledProcessError(retcode, cmd) > 00105: subprocess.CalledProcessError: Command ' srun `which > relion_autopick_mpi` --pickname autopick --odir "./" --particle_diameter > 666 --angpix 1.10410 --shrink 0.000 --gpu "" --ref > /scratch/project_2004278/ScipionUserData/projects/immTBEV/Runs/025798_ProtRelion2Autopick/reference_2d.stk > --angpix_ref 1.10000 --invert --ang 5 --lowpass 20 --i > input_micrographs.star --threshold 0.250 --min_distance -1.000 > --max_stddev_noise 1.100 --min_avg_noise -999.000' returned non-zero exit > status 143. > 00106: Protocol failed: Command ' srun `which relion_autopick_mpi` > --pickname autopick --odir "./" --particle_diameter 666 --angpix 1.10410 > --shrink 0.000 --gpu "" --ref > /scratch/project_2004278/ScipionUserData/projects/immTBEV/Runs/025798_ProtRelion2Autopick/reference_2d.stk > --angpix_ref 1.10000 --invert --ang 5 --lowpass 20 --i > input_micrographs.star --threshold 0.250 --min_distance -1.000 > --max_stddev_noise 1.100 --min_avg_noise -999.000' returned non-zero exit > status 143. > 00107: FAILED: pickMicrographStep, step 2, time 2022-01-17 > 15:25:37.465641 > 00108: *** Last status is failed > 00109: ------------------- PROTOCOL FAILED (DONE 2/2002) > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Pablo C. <pc...@cn...> - 2022-01-17 18:44:43
|
Hi Maria! It may be either: 1. Installation error 2. data related problem 3. a bug To discard 1, quite often is useful to run a related test For this, if you run: scipion3 tests --grep relion. You'll get lots of tests that relion plugin maintainer regularly run to ensure new changes does not break the functionality: scipion3 tests relion.tests.test_workflow_relion3 scipion3 tests relion.tests.test_workflow_relion3.TestWorkflowRelion3Betagal scipion3 tests relion.tests.test_protocols_relion3 scipion3 tests relion.tests.test_protocols_relion3.TestRelion31ImportParticles scipion3 tests relion.tests.test_protocols_relion3.Relion3TestMultiBody scipion3 tests relion.tests.test_protocols_relion3.Relion3TestMotioncor scipion3 tests relion.tests.test_protocols_relion3.Relion3TestAssignOptics scipion3 tests relion.tests.test_protocols_relion scipion3 tests relion.tests.test_protocols_relion.TestRelionSymmetrizeVolume scipion3 tests relion.tests.test_protocols_relion.TestRelionSubtract scipion3 tests relion.tests.test_protocols_relion.TestRelionResizeVolume scipion3 tests relion.tests.test_protocols_relion.TestRelionRemovePrefViews scipion3 tests relion.tests.test_protocols_relion.TestRelionRefine scipion3 tests relion.tests.test_protocols_relion.TestRelionPreprocess scipion3 tests relion.tests.test_protocols_relion.TestRelionPostprocess scipion3 tests relion.tests.test_protocols_relion.TestRelionPicking scipion3 tests relion.tests.test_protocols_relion.TestRelionLocalRes scipion3 tests relion.tests.test_protocols_relion.TestRelionInitialModel scipion3 tests relion.tests.test_protocols_relion.TestRelionExtractParticles scipion3 tests relion.tests.test_protocols_relion.TestRelionExportParticles scipion3 tests relion.tests.test_protocols_relion.TestRelionExportCtf scipion3 tests relion.tests.test_protocols_relion.TestRelionExpandSymmetry scipion3 tests relion.tests.test_protocols_relion.TestRelionCreate3dMask scipion3 tests relion.tests.test_protocols_relion.TestRelionClassify3D scipion3 tests relion.tests.test_protocols_relion.TestRelionClassify2D scipion3 tests relion.tests.test_protocols_relion.TestRelionCenterAverages scipion3 tests relion.tests.test_projection_subtraction_no_relion scipion3 tests relion.tests.test_projection_subtraction_no_relion.TestSubtractionProjection scipion3 tests relion.tests.test_convert_relion scipion3 tests relion.tests.test_convert_relion.TestRelionWriter scipion3 tests relion.tests.test_convert_relion.TestRelionReader scipion3 tests relion.tests.test_convert_relion.TestRelionOpticsGroups scipion3 tests relion.tests.test_convert_relion.TestReconstruct scipion3 tests relion.tests.test_convert_relion.TestConvertBinaryFiles scipion3 tests relion.tests.test_convert_relion.TestAlignment I'd choose --> scipion3 tests relion.tests.test_protocols_relion.TestRelionPicking To verify it works. If so, then we discard point 1. On 17/1/22 14:46, Anastasina, Maria wrote: > Dear colleagues, > > Relion auto-picking jobs within Scipion 3.0.8 fail with the error > message pasted below. I am picking particles using 2D averages as > references. These averages come from a different dataset than the > micrographs, and have been re-scaled to match the pixel size using > crop/resize protocol in Scipion. > > I don’t understand what exactly is going wrong and would be very > appreciative if any of you could suggest the reason for failure. > > Best regards, > Maria > > > 00001: RUNNING PROTOCOL ----------------- > 00002: Hostname: r15g05.bullx > 00003: PID: 135115 > 00004: pyworkflow: 3.0.16 > 00005: plugin: relion > 00006: plugin v: 3.1.1 > 00007: currentDir: > /scratch/project_2004278/ScipionUserData/projects/immTBEV > 00008: workingDir: Runs/025798_ProtRelion2Autopick > 00009: runMode: Continue > 00010: MPI: 4 > 00011: threads: 1 > 00012: Starting at step: 1 > 00013: Running steps > 00014: STARTED: convertInputStep, step 1, time 2022-01-17 > 15:15:42.193627 > 00015: FINISHED: convertInputStep, step 1, time 2022-01-17 > 15:15:42.565530 > 00016: STARTED: pickMicrographStep, step 2, time 2022-01-17 > 15:15:42.591236 > 00017: Picking micrograph: > Runs/000799_ProtMotionCorr/extra/GridSquare_29251179_Data_FoilHole_30265827_Data_29254225_29254227_20210330_060030_fractions_aligned_mic_DW.mrc > > 00018: Some paths do not exist in: /usr/local/cuda/lib64 > 00019: srun `which relion_autopick_mpi` --pickname autopick > --odir "./" --particle_diameter 666 --angpix 1.10410 --shrink 0.000 > --gpu "" --ref > /scratch/project_2004278/ScipionUserData/projects/immTBEV/Runs/025798_ProtRelion2Autopick/reference_2d.stk > --angpix_ref 1.10000 --invert --ang 5 --lowpass 20 --i > input_micrographs.star --threshold 0.250 --min_distance -1.000 > --max_stddev_noise 1.100 --min_avg_noise -999.000 > 00020: RELION version: 3.1.1 > 00021: Precision: BASE=double, CUDA-ACC=single > 00022: > 00023: === RELION MPI setup === > 00024: + Number of MPI processes = 5 > 00025: + Master (0) runs on host = r15g05.bullx > 00026: ================= > 00027: + Slave 1 runs on host = r15g05.bullx > 00028: + Slave 2 runs on host = r15g05.bullx > 00029: + Slave 3 runs on host = r15g05.bullx > 00030: + Slave 4 runs on host = r15g05.bullx > 00031: + Run autopicking on the following micrographs: > 00032: * mic_000007.mrc > 00033: WARNING!!! Pixel size in reference image header= 0 but you > have provided --angpix_ref 1.1 > 00034: + WARNING: Requested rescale of micrographs is 636 pixels. > The largest prime factor in FFTs is 53 > 00035: + WARNING: Will change rescaling of micrographs to 638 > pixels, because the prime factor then becomes 29 > 00036: + WARNING: add --skip_optimise_scale to your autopick > command to prevent rescaling > 00037: Initialising FFTs for the references and masks ... > 00038: 000/??? sec ~~(,_,"> [oo] > 00039: 2/ 2 sec > ............................................................~~(,_,"> > 00040: + Using GPU device: 0 on MPI node: 0 > 00041: + Using GPU device: 1 on MPI node: 1 > 00042: + Using GPU device: 2 on MPI node: 2 > 00043: + Using GPU device: 3 on MPI node: 3 > 00044: + Using GPU device: 0 on MPI node: 4 > 00045: Autopicking ... > 00046: 000/??? sec ~~(,_,"> [oo] > 00047: 6/ 6 sec > ............................................................~~(,_,"> > 00048: Generating logfile.pdf ... > 00049: 000/??? sec ~~(,_,"> [oo] > 00050: 0/ 0 sec > ............................................................~~(,_,"> > 00051: Total number of particles from 1 micrographs is 0 > 00052: i.e. on average there were 0 particles per micrograph > 00053: terminate called after throwing an instance of 'std::bad_alloc' > 00054: what(): std::bad_alloc > 00055: [r15g05:135359] *** Process received signal *** > 00056: [r15g05:135359] Signal: Aborted (6) > 00057: [r15g05:135359] Signal code: (-6) > 00058: [r15g05:135359] [ 0] > /lib64/libpthread.so.0(+0xf630)[0x7f0aad9e5630] > 00059: [r15g05:135359] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x7f0aa8d15387] > 00060: [r15g05:135359] [ 2] /lib64/libc.so.6(abort+0x148)[0x7f0aa8d16a78] > 00061: [r15g05:135359] [ 3] > /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x94983)[0x7f0aa9443983] > 00062: [r15g05:135359] [ 4] > /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x9aaf6)[0x7f0aa9449af6] > 00063: [r15g05:135359] [ 5] > /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x9ab31)[0x7f0aa9449b31] > 00064: [r15g05:135359] [ 6] > /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x9ad63)[0x7f0aa9449d63] > 00065: [r15g05:135359] [ 7] > /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x9b22c)[0x7f0aa944a22c] > 00066: [r15g05:135359] [ 8] > /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_+0x57)[0x7f0ab6c64b87] > 00067: [r15g05:135359] [ 9] > /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZN7CPlot2D23ComputeLabelTickSpacingEddPdS0_S0_iNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x315)[0x7f0ab6c626b5] > 00068: [r15g05:135359] [10] > /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZN7CPlot2D20PrecomputeDimensionsEv+0x489)[0x7f0ab6c62eb9] > 00069: [r15g05:135359] [11] > /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZN7CPlot2D20OutputPostScriptPlotENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x51)[0x7f0ab6c63441] > 00070: [r15g05:135359] [12] > /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZN10AutoPicker18generatePDFLogfileEv+0x762)[0x7f0ab6c849a2] > 00071: [r15g05:135359] [13] > /appl/soft/math/scipion/3.0.7/software/em/relion-3.1.0/bin/relion_autopick_mpi(main+0x11c)[0x4024ec] > 00072: [r15g05:135359] [14] > /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f0aa8d01555] > 00073: [r15g05:135359] [15] > /appl/soft/math/scipion/3.0.7/software/em/relion-3.1.0/bin/relion_autopick_mpi[0x4025dc] > 00074: [r15g05:135359] *** End of error message *** > 00075: srun: error: r15g05: task 0: Aborted > 00076: srun: launch/slurm: _step_signal: Terminating StepId=10234377.0 > 00077: slurmstepd: error: *** STEP 10234377.0 ON r15g05 CANCELLED AT > 2022-01-17T15:25:37 *** > 00078: srun: error: r15g05: tasks 1-4: Terminated > 00079: srun: Force Terminated StepId=10234377.0 > 00080: Traceback (most recent call last): > 00081: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 197, in run > 00082: self._run() > 00083: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 248, in _run > 00084: resultFiles = self._runFunc() > 00085: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 244, in _runFunc > 00086: return self._func(*self._args) > 00087: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_particles_picking.py", > line 241, in pickMicrographStep > 00088: self._pickMicrograph(mic, *args) > 00089: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/relion/protocols/protocol_autopick.py", > line 44, in _pickMicrograph > 00090: self._pickMicrographList([mic], *args) > 00091: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/relion/protocols/protocol_autopick.py", > line 54, in _pickMicrographList > 00092: self._pickMicrographsFromStar(micStar, micsDir, *args) > 00093: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/relion/protocols/protocol_autopick_ref.py", > line 401, in _pickMicrographsFromStar > 00094: self.runJob(program, params, cwd=cwd) > 00095: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 1389, in runJob > 00096: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) > 00097: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", > line 65, in runJob > 00098: process.runJob(log, programName, params, > 00099: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 52, in runJob > 00100: return runCommand(command, env, cwd) > 00101: File > "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 67, in runCommand > 00102: check_call(command, shell=True, stdout=sys.stdout, > stderr=sys.stderr, > 00103: File > "/appl/soft/math/scipion/3.8.7-gnu8.3.0/lib/python3.8/subprocess.py", > line 364, in check_call > 00104: raise CalledProcessError(retcode, cmd) > 00105: subprocess.CalledProcessError: Command ' srun `which > relion_autopick_mpi` --pickname autopick --odir "./" > --particle_diameter 666 --angpix 1.10410 --shrink 0.000 --gpu "" --ref > /scratch/project_2004278/ScipionUserData/projects/immTBEV/Runs/025798_ProtRelion2Autopick/reference_2d.stk > --angpix_ref 1.10000 --invert --ang 5 --lowpass 20 --i > input_micrographs.star --threshold 0.250 --min_distance -1.000 > --max_stddev_noise 1.100 --min_avg_noise -999.000' returned non-zero > exit status 143. > 00106: Protocol failed: Command ' srun `which relion_autopick_mpi` > --pickname autopick --odir "./" --particle_diameter 666 --angpix > 1.10410 --shrink 0.000 --gpu "" --ref > /scratch/project_2004278/ScipionUserData/projects/immTBEV/Runs/025798_ProtRelion2Autopick/reference_2d.stk > --angpix_ref 1.10000 --invert --ang 5 --lowpass 20 --i > input_micrographs.star --threshold 0.250 --min_distance -1.000 > --max_stddev_noise 1.100 --min_avg_noise -999.000' returned non-zero > exit status 143. > 00107: FAILED: pickMicrographStep, step 2, time 2022-01-17 > 15:25:37.465641 > 00108: *** Last status is failed > 00109: ------------------- PROTOCOL FAILED (DONE 2/2002) > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Anastasina, M. <mar...@he...> - 2022-01-17 14:19:38
|
Dear colleagues, Relion auto-picking jobs within Scipion 3.0.8 fail with the error message pasted below. I am picking particles using 2D averages as references. These averages come from a different dataset than the micrographs, and have been re-scaled to match the pixel size using crop/resize protocol in Scipion. I don’t understand what exactly is going wrong and would be very appreciative if any of you could suggest the reason for failure. Best regards, Maria 00001: RUNNING PROTOCOL ----------------- 00002: Hostname: r15g05.bullx 00003: PID: 135115 00004: pyworkflow: 3.0.16 00005: plugin: relion 00006: plugin v: 3.1.1 00007: currentDir: /scratch/project_2004278/ScipionUserData/projects/immTBEV 00008: workingDir: Runs/025798_ProtRelion2Autopick 00009: runMode: Continue 00010: MPI: 4 00011: threads: 1 00012: Starting at step: 1 00013: Running steps 00014: STARTED: convertInputStep, step 1, time 2022-01-17 15:15:42.193627 00015: FINISHED: convertInputStep, step 1, time 2022-01-17 15:15:42.565530 00016: STARTED: pickMicrographStep, step 2, time 2022-01-17 15:15:42.591236 00017: Picking micrograph: Runs/000799_ProtMotionCorr/extra/GridSquare_29251179_Data_FoilHole_30265827_Data_29254225_29254227_20210330_060030_fractions_aligned_mic_DW.mrc 00018: Some paths do not exist in: /usr/local/cuda/lib64 00019: srun `which relion_autopick_mpi` --pickname autopick --odir "./" --particle_diameter 666 --angpix 1.10410 --shrink 0.000 --gpu "" --ref /scratch/project_2004278/ScipionUserData/projects/immTBEV/Runs/025798_ProtRelion2Autopick/reference_2d.stk --angpix_ref 1.10000 --invert --ang 5 --lowpass 20 --i input_micrographs.star --threshold 0.250 --min_distance -1.000 --max_stddev_noise 1.100 --min_avg_noise -999.000 00020: RELION version: 3.1.1 00021: Precision: BASE=double, CUDA-ACC=single 00022: 00023: === RELION MPI setup === 00024: + Number of MPI processes = 5 00025: + Master (0) runs on host = r15g05.bullx 00026: ================= 00027: + Slave 1 runs on host = r15g05.bullx 00028: + Slave 2 runs on host = r15g05.bullx 00029: + Slave 3 runs on host = r15g05.bullx 00030: + Slave 4 runs on host = r15g05.bullx 00031: + Run autopicking on the following micrographs: 00032: * mic_000007.mrc 00033: WARNING!!! Pixel size in reference image header= 0 but you have provided --angpix_ref 1.1 00034: + WARNING: Requested rescale of micrographs is 636 pixels. The largest prime factor in FFTs is 53 00035: + WARNING: Will change rescaling of micrographs to 638 pixels, because the prime factor then becomes 29 00036: + WARNING: add --skip_optimise_scale to your autopick command to prevent rescaling 00037: Initialising FFTs for the references and masks ... 00038: 000/??? sec ~~(,_,"> [oo] 00039: 2/ 2 sec ............................................................~~(,_,"> 00040: + Using GPU device: 0 on MPI node: 0 00041: + Using GPU device: 1 on MPI node: 1 00042: + Using GPU device: 2 on MPI node: 2 00043: + Using GPU device: 3 on MPI node: 3 00044: + Using GPU device: 0 on MPI node: 4 00045: Autopicking ... 00046: 000/??? sec ~~(,_,"> [oo] 00047: 6/ 6 sec ............................................................~~(,_,"> 00048: Generating logfile.pdf ... 00049: 000/??? sec ~~(,_,"> [oo] 00050: 0/ 0 sec ............................................................~~(,_,"> 00051: Total number of particles from 1 micrographs is 0 00052: i.e. on average there were 0 particles per micrograph 00053: terminate called after throwing an instance of 'std::bad_alloc' 00054: what(): std::bad_alloc 00055: [r15g05:135359] *** Process received signal *** 00056: [r15g05:135359] Signal: Aborted (6) 00057: [r15g05:135359] Signal code: (-6) 00058: [r15g05:135359] [ 0] /lib64/libpthread.so.0(+0xf630)[0x7f0aad9e5630] 00059: [r15g05:135359] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x7f0aa8d15387] 00060: [r15g05:135359] [ 2] /lib64/libc.so.6(abort+0x148)[0x7f0aa8d16a78] 00061: [r15g05:135359] [ 3] /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x94983)[0x7f0aa9443983] 00062: [r15g05:135359] [ 4] /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x9aaf6)[0x7f0aa9449af6] 00063: [r15g05:135359] [ 5] /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x9ab31)[0x7f0aa9449b31] 00064: [r15g05:135359] [ 6] /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x9ad63)[0x7f0aa9449d63] 00065: [r15g05:135359] [ 7] /appl/spack/install-tree/gcc-4.8.5/gcc-8.3.0-qzmzn5/lib64/libstdc++.so.6(+0x9b22c)[0x7f0aa944a22c] 00066: [r15g05:135359] [ 8] /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_+0x57)[0x7f0ab6c64b87] 00067: [r15g05:135359] [ 9] /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZN7CPlot2D23ComputeLabelTickSpacingEddPdS0_S0_iNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x315)[0x7f0ab6c626b5] 00068: [r15g05:135359] [10] /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZN7CPlot2D20PrecomputeDimensionsEv+0x489)[0x7f0ab6c62eb9] 00069: [r15g05:135359] [11] /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZN7CPlot2D20OutputPostScriptPlotENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x51)[0x7f0ab6c63441] 00070: [r15g05:135359] [12] /appl/soft/math/relion/relion-3.1.1-gpubuild/lib/librelion_lib.so(_ZN10AutoPicker18generatePDFLogfileEv+0x762)[0x7f0ab6c849a2] 00071: [r15g05:135359] [13] /appl/soft/math/scipion/3.0.7/software/em/relion-3.1.0/bin/relion_autopick_mpi(main+0x11c)[0x4024ec] 00072: [r15g05:135359] [14] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f0aa8d01555] 00073: [r15g05:135359] [15] /appl/soft/math/scipion/3.0.7/software/em/relion-3.1.0/bin/relion_autopick_mpi[0x4025dc] 00074: [r15g05:135359] *** End of error message *** 00075: srun: error: r15g05: task 0: Aborted 00076: srun: launch/slurm: _step_signal: Terminating StepId=10234377.0 00077: slurmstepd: error: *** STEP 10234377.0 ON r15g05 CANCELLED AT 2022-01-17T15:25:37 *** 00078: srun: error: r15g05: tasks 1-4: Terminated 00079: srun: Force Terminated StepId=10234377.0 00080: Traceback (most recent call last): 00081: File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run 00082: self._run() 00083: File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run 00084: resultFiles = self._runFunc() 00085: File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc 00086: return self._func(*self._args) 00087: File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_particles_picking.py", line 241, in pickMicrographStep 00088: self._pickMicrograph(mic, *args) 00089: File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/relion/protocols/protocol_autopick.py", line 44, in _pickMicrograph 00090: self._pickMicrographList([mic], *args) 00091: File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/relion/protocols/protocol_autopick.py", line 54, in _pickMicrographList 00092: self._pickMicrographsFromStar(micStar, micsDir, *args) 00093: File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/relion/protocols/protocol_autopick_ref.py", line 401, in _pickMicrographsFromStar 00094: self.runJob(program, params, cwd=cwd) 00095: File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1389, in runJob 00096: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) 00097: File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob 00098: process.runJob(log, programName, params, 00099: File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob 00100: return runCommand(command, env, cwd) 00101: File "/appl/soft/math/scipion/3.0.7/.scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand 00102: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, 00103: File "/appl/soft/math/scipion/3.8.7-gnu8.3.0/lib/python3.8/subprocess.py", line 364, in check_call 00104: raise CalledProcessError(retcode, cmd) 00105: subprocess.CalledProcessError: Command ' srun `which relion_autopick_mpi` --pickname autopick --odir "./" --particle_diameter 666 --angpix 1.10410 --shrink 0.000 --gpu "" --ref /scratch/project_2004278/ScipionUserData/projects/immTBEV/Runs/025798_ProtRelion2Autopick/reference_2d.stk --angpix_ref 1.10000 --invert --ang 5 --lowpass 20 --i input_micrographs.star --threshold 0.250 --min_distance -1.000 --max_stddev_noise 1.100 --min_avg_noise -999.000' returned non-zero exit status 143. 00106: Protocol failed: Command ' srun `which relion_autopick_mpi` --pickname autopick --odir "./" --particle_diameter 666 --angpix 1.10410 --shrink 0.000 --gpu "" --ref /scratch/project_2004278/ScipionUserData/projects/immTBEV/Runs/025798_ProtRelion2Autopick/reference_2d.stk --angpix_ref 1.10000 --invert --ang 5 --lowpass 20 --i input_micrographs.star --threshold 0.250 --min_distance -1.000 --max_stddev_noise 1.100 --min_avg_noise -999.000' returned non-zero exit status 143. 00107: FAILED: pickMicrographStep, step 2, time 2022-01-17 15:25:37.465641 00108: *** Last status is failed 00109: ------------------- PROTOCOL FAILED (DONE 2/2002) |
|
From: Dmitry A. S. <sem...@gm...> - 2021-12-20 18:22:36
|
Great present to all users for Christmas 🎄! Thank you @Scipion&Xmipp team, thank you Pablo! Merry Christmas& Happy New Year to all! Sincerely, Dmitry. P.s. I have already noticed on the course that the Scipion version we used was +1 number ahead of mine. Now my curiosity is satisfied. On December 20, 2021 6:27:24 PM Pablo Conesa <pc...@cn...> wrote: > Dear users, we have today released some updates for "the core" > (scipion-pyworkflow, scipion-em and scipion-app) > > Here are the release notes: > > https://github.com/scipion-em/docs/blob/release-3.0.0/docs/developer/release-notes.rst#v3018-2021-12-20-core-or-pworkflow > > > > > Main new functionality added is: > > Possible outputs definition is now possible. Protocols can define possible > outputs to allow designing a workflow in advance without executing them. > > Workflow templates can now be imported into an existing project > > > > > > -- > > Pablo Conesa - Madrid Scipion team > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Pablo C. <pc...@cn...> - 2021-12-20 17:27:01
|
Dear users, we have today released some updates for "the core" (scipion-pyworkflow, scipion-em and scipion-app) Here are the release notes: https://github.com/scipion-em/docs/blob/release-3.0.0/docs/developer/release-notes.rst#v3018-2021-12-20-core-or-pworkflow Main new functionality added is: Possible outputs definition is now possible. Protocols can define possible outputs to allow designing a workflow in advance without executing them. Workflow templates can now be imported into an existing project -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Pablo C. <pc...@cn...> - 2021-12-10 19:51:22
|
Yes, that behaviour is correct, we do not want all users to start using "alpha close to beta" code, so is not available in the plugin manager. On 10/12/21 15:54, Coudray, Nicolas via scipion-users wrote: > > Hi Pablo, > > > Thanks a lot for the reply. I tried the devel installation. It seems > to run correctly, although it still doesn't appear in the "plugin > manager", I can now see the dynamo tools once I open a project (but > maybe that's intended for devel plugins). > > > Thanks again. Looking forward to the next stable version : -) > > Best regards, > Nicolas > > ------------------------------------------------------------------------ > *From:* Pablo Conesa <pc...@cn...> > *Sent:* Friday, December 10, 2021 3:26 AM > *To:* sci...@li... > *Subject:* Re: [scipion-users] installation of dynamo plugin > > *[EXTERNAL]* > > Hi Nicolas, bear in mind that tomography plugin are still in alpha. I > hope not for long. > > > Nevertheless, we are having a workshop next week and all seems quite > stable. > > If you still want to go ahead, my guess is that you might have not > installed the plugin in devel mode. > > please do this: > > scipion3 installp -p > /usr/local/scipion/source/plugins/scipion-em-dynamo --devel > > Let us know how it goes. > > On 9/12/21 22:08, Coudray, Nicolas via scipion-users wrote: >> >> Hi, >> >> >> We have a Centos workstation with Scipion installed, but I have >> trouble installing and using the dynamo plugin. >> >> >> >> We have: >> >> /*# scipion version >> Scipion v3.0.9 - Eugenius >> pyworkflow - 3.0.17 >> pwem - 3.0.13*/ >> >> I tried to follow the instruction on the dynamo github page and the >> scipion one, but still have trouble. >> >> Currently, I have the plugin in the scipion folder: >> >> /*# cd scipion-em-dynamo >> # pwd >> /usr/local/scipion/source/plugins/scipion-em-dynamo >> # ls >> CHANGES.txt dynamo LICENSE MANIFEST.in README.rst >> requirements.txt scipion_em_dynamo.egg-info setup.py*/ >> >> and when I run >> */scipion installb --help >> /*I see down in the lines: >> */dynamo 1.146 [X] >> /* >> >> However, when I launch scipion and start a project, I don't see the >> dynamo plugin. If I open the plugin manager, I don't see it either in >> the list. >> >> Any help would be welcome >> >> Thanks, >> Best, >> Nicolas >> >> >> >> >> >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > -- > Pablo Conesa - *Madrid Scipion > <https://urldefense.com/v3/__http://scipion.i2pc.es__;!!MXfaZl3l!MG8I2YUoC-_5O1WFikqaq8djJvmvI7lUhcARIg1T_kjyijOO0pMoqAU4iHkIhesdP0e5WNbV$> > team* > > > ------------------------------------------------------------ > This email message, including any attachments, is for the sole use of > the intended recipient(s) and may contain information that is > proprietary, confidential, and exempt from disclosure under applicable > law. Any unauthorized review, use, disclosure, or distribution is > prohibited. If you have received this email in error please notify the > sender by return email and delete the original message. Please note, > the recipient should check this email and any attachments for the > presence of viruses. The organization accepts no liability for any > damage caused by any virus transmitted by this email. > ================================= > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Marc H. L. <mh...@ib...> - 2021-12-10 15:42:57
|
Hi Alberto! Sorry to answer late, I have tried the instructions and in the end I was also missing a repository: - libsqlite3x.x86_64 libsqlite3x-devel.x86_64 Thank you very much for the help. Now it was installed fine! Best regards, El mar, 30 nov 2021 a las 14:25, Alberto Garcia Mena (< alb...@cn...>) escribió: > Hello Marc Hsiao Le, > > There is an installation guide for Centos7 > <https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-CentOS-7-9.2009>, > please follow those steps in that order; first install openmpi-devel, then > the compilers (gcc g++). > On 30/11/21 11:24, Marc Hsiao Lee wrote: > > Hi guys! > > I hope someone can help me, I have the Centos8 version, and I'm standing > at this point with conda: > > - python -m scipion installp -p scipion-em-xmipp -j 12 > > and the error output is: > > ... > * mpirun or mpiexec have failed.* > * Cannot compile with MPI or use it* > * rm xmipp_mpi_test_main** > *rm: cannot remove 'xmipp_mpi_test_main*': No such file or directory* > > *Check failed! Something wrong with the configuration.* > > > *Traceback (most recent call last):* > * File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module>* > * main()* > * File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main* > * installPluginMethods()* > * File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods* > * plugin.installBin({'args': ['-j', numberProcessor]})* > * File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin* > * environment.execute()* > * File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute* > * self._executeTargets(targetList)* > * File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets* > * tgt.execute()* > * File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute* > * command.execute()* > * File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute* > * assert glob(t), ("target '%s' not built (after "* > *AssertionError: target > '/cryoem-apps/scipion/scipion3.0/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=12 && ln -srfn build > /cryoem-apps/scipion/scipion3.0/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null')* > *Error at main: target > '/cryoem-apps/scipion/scipion3.0/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=12 && ln -srfn build > /cryoem-apps/scipion/scipion3.0/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null')* > > > Thanks and regards > -- > > [image: IBMB - Institut de Biología Molecular de Barcelona] > > <http://linkedin.com/company/ibmb> <https://www.instagram.com/ibmb_csic_/> > <https://www.facebook.com/IBMB.CSIC.es> <https://twitter.com/IBMB_CSIC> [image: > youtube] > <https://www.youtube.com/channel/UCxIFUCBs2RKA1Mp_AXrrO7w/featured> > <https://www.csic.es/> > > Marcos H.Lee > > IBMB-CSIC > > E-mail: mh...@ib... > > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > - Alberto GM - > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > -- [image: IBMB - Institut de Biología Molecular de Barcelona] <https://www.ibmb.csic.es/en/> Marcos H.Lee IBMB-CSIC E-mail: mh...@ib... |
|
From: Coudray, N. <Nic...@ny...> - 2021-12-10 15:19:24
|
Hi Pablo, Thanks a lot for the reply. I tried the devel installation. It seems to run correctly, although it still doesn't appear in the "plugin manager", I can now see the dynamo tools once I open a project (but maybe that's intended for devel plugins). Thanks again. Looking forward to the next stable version : -) Best regards, Nicolas ________________________________ From: Pablo Conesa <pc...@cn...> Sent: Friday, December 10, 2021 3:26 AM To: sci...@li... Subject: Re: [scipion-users] installation of dynamo plugin [EXTERNAL] Hi Nicolas, bear in mind that tomography plugin are still in alpha. I hope not for long. Nevertheless, we are having a workshop next week and all seems quite stable. If you still want to go ahead, my guess is that you might have not installed the plugin in devel mode. please do this: scipion3 installp -p /usr/local/scipion/source/plugins/scipion-em-dynamo --devel Let us know how it goes. On 9/12/21 22:08, Coudray, Nicolas via scipion-users wrote: Hi, We have a Centos workstation with Scipion installed, but I have trouble installing and using the dynamo plugin. We have: # scipion version Scipion v3.0.9 - Eugenius pyworkflow - 3.0.17 pwem - 3.0.13 I tried to follow the instruction on the dynamo github page and the scipion one, but still have trouble. Currently, I have the plugin in the scipion folder: # cd scipion-em-dynamo # pwd /usr/local/scipion/source/plugins/scipion-em-dynamo # ls CHANGES.txt dynamo LICENSE MANIFEST.in README.rst requirements.txt scipion_em_dynamo.egg-info setup.py and when I run scipion installb --help I see down in the lines: dynamo 1.146 [X] However, when I launch scipion and start a project, I don't see the dynamo plugin. If I open the plugin manager, I don't see it either in the list. Any help would be welcome Thanks, Best, Nicolas _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users<https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/scipion-users__;!!MXfaZl3l!MG8I2YUoC-_5O1WFikqaq8djJvmvI7lUhcARIg1T_kjyijOO0pMoqAU4iHkIhesdPxRuhmEc$> -- Pablo Conesa - Madrid Scipion<https://urldefense.com/v3/__http://scipion.i2pc.es__;!!MXfaZl3l!MG8I2YUoC-_5O1WFikqaq8djJvmvI7lUhcARIg1T_kjyijOO0pMoqAU4iHkIhesdP0e5WNbV$> team ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= |
|
From: Pablo C. <pc...@cn...> - 2021-12-10 08:26:48
|
Hi Nicolas, bear in mind that tomography plugin are still in alpha. I hope not for long. Nevertheless, we are having a workshop next week and all seems quite stable. If you still want to go ahead, my guess is that you might have not installed the plugin in devel mode. please do this: scipion3 installp -p /usr/local/scipion/source/plugins/scipion-em-dynamo --devel Let us know how it goes. On 9/12/21 22:08, Coudray, Nicolas via scipion-users wrote: > > Hi, > > > We have a Centos workstation with Scipion installed, but I have > trouble installing and using the dynamo plugin. > > > > We have: > > /*# scipion version > Scipion v3.0.9 - Eugenius > pyworkflow - 3.0.17 > pwem - 3.0.13*/ > > I tried to follow the instruction on the dynamo github page and the > scipion one, but still have trouble. > > Currently, I have the plugin in the scipion folder: > > /*# cd scipion-em-dynamo > # pwd > /usr/local/scipion/source/plugins/scipion-em-dynamo > # ls > CHANGES.txt dynamo LICENSE MANIFEST.in README.rst > requirements.txt scipion_em_dynamo.egg-info setup.py*/ > > and when I run > */scipion installb --help > /*I see down in the lines: > */dynamo 1.146 [X] > /* > > However, when I launch scipion and start a project, I don't see the > dynamo plugin. If I open the plugin manager, I don't see it either in > the list. > > Any help would be welcome > > Thanks, > Best, > Nicolas > > > > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Coudray, N. <Nic...@ny...> - 2021-12-09 21:34:12
|
Hi, We have a Centos workstation with Scipion installed, but I have trouble installing and using the dynamo plugin. We have: # scipion version Scipion v3.0.9 - Eugenius pyworkflow - 3.0.17 pwem - 3.0.13 I tried to follow the instruction on the dynamo github page and the scipion one, but still have trouble. Currently, I have the plugin in the scipion folder: # cd scipion-em-dynamo # pwd /usr/local/scipion/source/plugins/scipion-em-dynamo # ls CHANGES.txt dynamo LICENSE MANIFEST.in README.rst requirements.txt scipion_em_dynamo.egg-info setup.py and when I run scipion installb --help I see down in the lines: dynamo 1.146 [X] However, when I launch scipion and start a project, I don't see the dynamo plugin. If I open the plugin manager, I don't see it either in the list. Any help would be welcome Thanks, Best, Nicolas |
|
From: Carlos H. F. <car...@so...> - 2021-12-08 16:43:15
|
Dear all,
I'm trying to run a 2D classification using cryosparc inside Scipion and I'm facing the error below?
Does anyone have any idea what this error might be?
Thanks in advance,
Carlos Fernandes
Traceback (most recent call last):
00002: File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 201, in run
00003: self._run()
00004: File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 252, in _run
00005: resultFiles = self._runFunc()
00006: File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _runFunc
00007: return self._func(*self._args)
00008: File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_base.py", line 97, in convertInputStep
00009: self._importParticles()
00010: File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_base.py", line 200, in _importParticles
00011: self.importedParticles = doImportParticlesStar(self)
00012: File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/cryosparc2/utils.py", line 306, in doImportParticlesStar
00013: import_particles = enqueueJob(className, protocol.projectName, protocol.workSpaceName,
00014: File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/cryosparc2/utils.py", line 385, in enqueueJob
00015: exitCode, cmdOutput = runCmd(make_job_cmd)
00016: File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/cryosparc2/utils.py", line 442, in runCmd
00017: raise Exception("%s failed --> Exit code %s, message %s" % (cmd, exitCode, cmdOutput))
00018: Exception: /home/impmc/cryosparc_new/cryosparc_master/bin/cryosparcm cli 'make_job("import_particles","P3","W2", "", "None", "None", {"particle_meta_path": "/mnt/data1/mauricio/cyclo-pasteur/scipion/Cyclodextrine/Runs/002524_ProtCryo2D/tmp/input_particles.star", "particle_blob_path": "/mnt/data1/mauricio/cyclo-pasteur/scipion/Cyclodextrine/Runs/002524_ProtCryo2D/tmp", "psize_A": "0.86"}, {}, "False", 0)' failed --> Exit code 1, message Traceback (most recent call last):
00019: File "/home/impmc/cryosparc_new/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/runpy.py", line 193, in _run_module_as_main
00020: "__main__", mod_spec)
00021: File "/home/impmc/cryosparc_new/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/runpy.py", line 85, in _run_code
00022: exec(code, run_globals)
00023: File "/home/impmc/cryosparc_new/cryosparc_master/cryosparc_compute/client.py", line 91, in <module>
00024: print(eval("cli."+command))
00025: File "<string>", line 1, in <module>
00026: File "/home/impmc/cryosparc_new/cryosparc_master/cryosparc_compute/client.py", line 64, in func
00027: assert False, res['error']
00028: AssertionError: {'code': 500, 'data': None, 'message': "OtherError: argument of type 'NoneType' is not iterable", 'name': 'OtherError'}
00029: Protocol failed: /home/impmc/cryosparc_new/cryosparc_master/bin/cryosparcm cli 'make_job("import_particles","P3","W2", "", "None", "None", {"particle_meta_path": "/mnt/data1/mauricio/cyclo-pasteur/scipion/Cyclodextrine/Runs/002524_ProtCryo2D/tmp/input_particles.star", "particle_blob_path": "/mnt/data1/mauricio/cyclo-pasteur/scipion/Cyclodextrine/Runs/002524_ProtCryo2D/tmp", "psize_A": "0.86"}, {}, "False", 0)' failed --> Exit code 1, message Traceback (most recent call last):
00030: File "/home/impmc/cryosparc_new/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/runpy.py", line 193, in _run_module_as_main
00031: "__main__", mod_spec)
00032: File "/home/impmc/cryosparc_new/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/runpy.py", line 85, in _run_code
00033: exec(code, run_globals)
00034: File "/home/impmc/cryosparc_new/cryosparc_master/cryosparc_compute/client.py", line 91, in <module>
00035: print(eval("cli."+command))
00036: File "<string>", line 1, in <module>
00037: File "/home/impmc/cryosparc_new/cryosparc_master/cryosparc_compute/client.py", line 64, in func
00038: assert False, res['error']
00039: AssertionError: {'code': 500, 'data': None, 'message': "OtherError: argument of type 'NoneType' is not iterable", 'name': 'OtherError'}
|
|
From: Alberto G. M. <alb...@cn...> - 2021-11-30 13:23:48
|
Hello Marc Hsiao Le, There is aninstallation guide for Centos7 <https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-CentOS-7-9.2009>, please follow those steps in that order; first install openmpi-devel, then the compilers (gcc g++). On 30/11/21 11:24, Marc Hsiao Lee wrote: > Hi guys! > > I hope someone can help me, I have the Centos8 version, and I'm > standing at this point with conda: > > * python -m scipion installp -p scipion-em-xmipp -j 12 > > and the error output is: > > ... > * mpirun or mpiexec have failed.* > * Cannot compile with MPI or use it* > * rm xmipp_mpi_test_main** > *rm: cannot remove 'xmipp_mpi_test_main*': No such file or directory* > /*Check failed! Something wrong with the configuration.*/ > > / > / > > /Traceback (most recent call last):/ > / File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module>/ > / main()/ > / File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main/ > / installPluginMethods()/ > / File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods/ > / plugin.installBin({'args': ['-j', numberProcessor]})/ > / File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin/ > / environment.execute()/ > / File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute/ > / self._executeTargets(targetList)/ > / File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets/ > / tgt.execute()/ > / File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute/ > / command.execute()/ > / File > "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute/ > / assert glob(t), ("target '%s' not built (after "/ > /AssertionError: target > '/cryoem-apps/scipion/scipion3.0/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=12 && ln -srfn build > /cryoem-apps/scipion/scipion3.0/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null')/ > /Error at main: target > '/cryoem-apps/scipion/scipion3.0/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=12 && ln -srfn build > /cryoem-apps/scipion/scipion3.0/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null')/ > > / > / > Thanks and regards > -- > > IBMB - Institut de Biología Molecular de Barcelona > > <http://linkedin.com/company/ibmb><https://www.instagram.com/ibmb_csic_/> > <https://www.facebook.com/IBMB.CSIC.es> > <https://twitter.com/IBMB_CSIC>youtube > <https://www.youtube.com/channel/UCxIFUCBs2RKA1Mp_AXrrO7w/featured><https://www.csic.es/> > > > > Marcos H.Lee > > IBMB-CSIC > > E-mail: mh...@ib... <mailto:mh...@ib...> > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- - Alberto GM - |
|
From: Marc H. L. <mh...@ib...> - 2021-11-30 10:52:07
|
Hi guys!
I hope someone can help me, I have the Centos8 version, and I'm standing at
this point with conda:
- python -m scipion installp -p scipion-em-xmipp -j 12
and the error output is:
...
* mpirun or mpiexec have failed.*
* Cannot compile with MPI or use it*
* rm xmipp_mpi_test_main**
*rm: cannot remove 'xmipp_mpi_test_main*': No such file or directory*
*Check failed! Something wrong with the configuration.*
*Traceback (most recent call last):*
* File
"/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
line 470, in <module>*
* main()*
* File
"/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
line 293, in main*
* installPluginMethods()*
* File
"/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py",
line 232, in installPluginMethods*
* plugin.installBin({'args': ['-j', numberProcessor]})*
* File
"/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py",
line 166, in installBin*
* environment.execute()*
* File
"/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
line 748, in execute*
* self._executeTargets(targetList)*
* File
"/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
line 690, in _executeTargets*
* tgt.execute()*
* File
"/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
line 221, in execute*
* command.execute()*
* File
"/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
line 161, in execute*
* assert glob(t), ("target '%s' not built (after "*
*AssertionError: target
'/cryoem-apps/scipion/scipion3.0/software/em/xmipp/bin/xmipp_reconstruct_significant'
not built (after running 'cd . && ./xmipp config noAsk && ./xmipp
check_config && ./xmipp compileAndInstall N=12 && ln -srfn build
/cryoem-apps/scipion/scipion3.0/software/em/xmipp && cd - && touch
installation_finished && rm bindings_linked 2> /dev/null')*
*Error at main: target
'/cryoem-apps/scipion/scipion3.0/software/em/xmipp/bin/xmipp_reconstruct_significant'
not built (after running 'cd . && ./xmipp config noAsk && ./xmipp
check_config && ./xmipp compileAndInstall N=12 && ln -srfn build
/cryoem-apps/scipion/scipion3.0/software/em/xmipp && cd - && touch
installation_finished && rm bindings_linked 2> /dev/null')*
Thanks and regards
--
[image: IBMB - Institut de Biología Molecular de Barcelona]
<http://linkedin.com/company/ibmb> <https://www.instagram.com/ibmb_csic_/>
<https://www.facebook.com/IBMB.CSIC.es>
<https://twitter.com/IBMB_CSIC> [image:
youtube] <https://www.youtube.com/channel/UCxIFUCBs2RKA1Mp_AXrrO7w/featured>
<https://www.csic.es/>
Marcos H.Lee
IBMB-CSIC
E-mail: mh...@ib...
|
|
From: 范宏成 <187...@16...> - 2021-11-28 05:48:28
|
Dear David, Thank you so much for providing the Zernike3D information. I will read this paper and try relevant protocols in scipion3. Best regards, Hongcheng Fan | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 On 11/26/2021 23:06，David Herreros<dhe...@cn...> wrote： Dear Hongcheng, Protocols labeled as "Zernike3D" refer to a set of new tools to analyze continuous heterogeneity of molecules through CryoEM data at the level of maps and images (images tools are still in a beta state). You can find the full details of this new algorithm in our recent publication: IUCrJ. 2021 Oct 14;8(Pt 6):992-1005. doi: 10.1107/S2052252521008903. eCollection 2021 Nov 1. Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials. David Herreros, Roy R Lederman, James Krieger, Amaya Jiménez-Moreno, Marta Martínez, David Myška, David Strelak, Jiri Filipovic, Ivet Bahar, Jose Maria Carazo, Carlos Oscar S Sanchez Regarding the DeepAlign program, I am not sure if it has been included in this release. Probably Pablo, Grigory, or Alberto can give us more details about the availability of this program in Scipion. Kind regards, David Herreros |
|
From: Slavica J. <sla...@up...> - 2021-11-27 12:12:00
|
Dear Lizelle,
Thanks for your email and for using HEMNMA (and, more generally,
ContinuousFlex plugin of Scipion). Here are a few hints and
recommendations. If you need more help, let me know by emailing me directly.
*1) Visualization of normal-mode animations:*
In Scipion, VMD is the only option for visualizing normal-mode animations.
However, you can download the animations saved on your distant computer and
visualize them on your local computer using VMD if you have it installed. I
will give you some instructions here on what to do in both cases.
For playing animations with VMD in Scipion:
----------------------------------------------------------
The problem with VMD on your distant computer may be either related to (1)
a slow connection from your local computer (if you see that VMD is trying
to open the animation but it is taking too long and the animation cannot
open at the end) or to (2) a missing path to the VMD binary in the
configuration file of Scipion (check ~/scipion3/config/scipion.conf and add
the path to VMD binary that you will get using "which vmd" on a command
line of a terminal; for instance, if this command is giving you
"/usr/local/bin/vmd", it means that the binary is in "/usr/local/bin" in
which case you would add "VMD_HOME = /usr/local/bin" to scipion.conf, but
without quote marks).
For downloading animations from your distant computer and playing them with
VMD on your local computer (Scipion is not required for this):
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
All calculated animations are saved on the following path on your distant
computer (assuming ScipionUserData is in your home directory):
~/ScipionUserData/projects/NAME_OF_YOUR_PROJECT/Runs/XXXXXX_FlexProtNMA/extra/animations
Note that "NAME_OF_YOUR_PROJECT" should be replaced by the name you gave to
your project when creating it in Scipion. Aslo, "XXXXXX" should be replaced
by the run number that was automatically assigned by Scipion when you
started this NMA run.
For each normal mode, you will see two files: *.vmd and *.pdb (only the
normal modes higher than mode 7 are animated, as the first 6 modes should
not be used with HEMNMA). The file with the extension "pdb" (*.pdb) is the
animated PDB that VMD knows to play even without a dedicated vmd script
(the file with "vmd" extension, i.e., *.vmd). You can download all these
animations and play them on your local computer if you have VMD installed
on it. Load one *.pdb using "New Molecule" in "File" menu of VMD, press the
play button of VMD and the animation will start. If you wish a nicer
graphical representation, you may use the associated *.vmd script for this,
but you should replace the first line of this script by the path on which
the animation is located locally on your computer. For instance, you may
replace the first line of animated_mode_007.vmd by "mol new
./animated_mode_007.pdb", without quote marks, if you wish to open it with
VMD from the directory in which you downloaded the animations; then, you
will load this animated_mode_007.vmd via "Load Visualization State" in File
menu of VMD, which will start playing the animation automatically using a
nicer graphical representation of your molecule.
*2) Efficiency of image analysis using normal modes:*
There is no GPU processing in HEMNMA. Regarding CPUs, it is not clear to me
whether you have a cluster with 24 processors Intel(R) Xeon(R) Silver
4214R, meaning that you can use up to 576 threads on this cluster (24 x 24,
as each of the Intel(R) Xeon(R) Silver 4214R processors can use up to 24
threads).
To get a quick view of the continuous heterogeneity in your dataset, you do
not need to process the entire stack of ~100k particles and you may resize
them by binning them by 2 or 4 as I will explain below (but not window
them, as this may cut out your particles). We could notice that a subset of
10k-20k particles is enough to examine the degree of the heterogeneity of a
larger dataset. How much to bin depends on how coarse and quickly you want
to explore the heterogeneity, but also on the amplitude of the
conformational change of your molecule. Let me explain this via these 2
points:
2.1 HEMNMA involves a 2-level multiresolution-pyramid image analysis. For
an input image of size N x N pixels, this means that HEMNMA first analyzes
the same image at a coarser resolution (N/2 x N/2 pixels) and then
propagates the result obtained quickly at this level onto the original-size
image level (N x N pixels) to refine the result. Depending on the degree of
the flexibility of the molecule, it may or may not be Ok to provide HEMNMA
with images of size 64 x 64 pixels (the conformational variability should
be detectable at the coarser level of 32 x 32 pixels that HEMNMA will
internally use). If conformational variability is likely to be detected at
the coarser level of 32 x 32 pixels used by HEMNMA internally (because the
amplitude of the conformational change is large), then you may input 64x64
pixel images to HEMNMA.
2.2 In HEMNMA graphical interface, you need to choose the rigid-body
alignment method ("projection matching" or "wavelets & splines") to use in
combination with the elastic alignment based on normal modes. The
"projection matching" method is faster but less robust to noise than the
"wavelets & splines" method. Additionally, it is useful to know that
"wavelets & splines" requires a power of 2 size of the image, meaning that
you may resize your image to 128 or 64 pixels but not to 100 pixels. With
"projection matching", there is no such restriction (you may input images
of size of 100 x 100 pixels, which may be interesting in your case).
It should be noted that the image resizing can be done directly with HEMNMA
graphical interface (step "Resize particles"). Note also that HEMNMA
currently allows entering individual particle images as well (beside a
stack form of input images). Although it may be interesting (or enough) to
first see the heterogeneity of a smaller subset of your full dataset (as I
said, 10-20k particles), you should also know that there are ways to split
your full (large) stack in several pieces and run these pieces on several
separate computers or run many parallel jobs on a supercomputer (each job
on a different piece of the stack) and then combine the results of the runs
on different pieces of the stack. The combined result file can later be
analyzed with HEMNMA graphical interface (the field "Precomputed results"
of the black/step "Image analysis with normal modes" that you can visualize
using "Advanced" button in "Expert level").
Last but not least, HEMNMA is part of ContinuousFlex plugin of Scipion (
https://github.com/scipion-em/scipion-em-continuousflex). We are regularly
updating this plugin and integrating new protocols, for SPA and ET. I would
like to invite you to update ContinuousFlex plugin in your Scipion
installation whenever the new updates become available (when an update is
available, red letters appear when you click on "scipion-em-continuousflex"
in Scipion's Plugin Manager).
I hope this helps. Let me know if you have any further questions.
Regards,
Slavica
On Wed, Nov 24, 2021 at 4:05 PM Carlos Oscar Sorzano <co...@cn...>
wrote:
> Dear Lizelle,
>
>
> I am forwarding your mail to Slavica, who is the person in charge of
> ContinuousFlex.
>
>
> Kind regards, Carlos Oscar
>
>
> El 24/11/2021 a las 15:58, Lizelle Lubbe via scipion-users escribió:
>
> Hi everyone,
>
> I would like to run HEMNMA on my particles and have done the NMA step
> using an atomic model. Is there any way to visualize the trajectories other
> than through VMD in Scipion? I am accessing the campus computer with
> Scipion remotely and it seems like VMD installation may be an issue.
>
> Three modes from an input PDB show high collectivity with low scores and I
> would like to now try NMA alignment with these modes. Given the high
> computational cost of the protocol, is it recommended to use a subset of
> particles for the analysis at present? The original stack is of ~100k
> particles (discrete heterogeneity was removed by 2 rounds of 2D
> classification and some 3D classifications but there is still continuous
> heterogeneity). It would be great to see the full range of variations with
> all particles but maybe not computationally feasible at present? The box
> size at 1.06A/pix is 256 so I can maybe bin by 4 to 64pix but windowing
> further will cut into my particle.
>
> We have 256GB RAM with 24 Intel(R) Xeon(R) Silver 4214R CPU @ 2.40GHz and
> 4 Quadro RTX 5000 GPUs.
>
> Kind regards,
> Lizelle
> Disclaimer - University of Cape Town This email is subject to UCT policies
> and email disclaimer published on our website at
> http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650
> 9111. If this email is not related to the business of UCT, it is sent by
> the sender in an individual capacity. Please report security incidents or
> abuse via https://csirt.uct.ac.za/page/report-an-incident.php.
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
|
|
From: David H. <dhe...@cn...> - 2021-11-26 15:06:24
|
Dear Hongcheng,
Protocols labeled as "Zernike3D" refer to a set of new tools to analyze
continuous heterogeneity of molecules through CryoEM data at the level
of maps and images (images tools are still in a beta state). You can
find the full details of this new algorithm in our recent publication:
IUCrJ. 2021 Oct 14;8(Pt 6):992-1005.
doi: 10.1107/S2052252521008903. eCollection 2021 Nov 1.
Approximating deformation fields for the analysis of continuous
heterogeneity of biological macromolecules by 3D Zernike
polynomials. David Herreros, Roy R Lederman, James Krieger, Amaya
Jiménez-Moreno, Marta Martínez, David Myška, David Strelak, Jiri
Filipovic, Ivet Bahar, Jose Maria Carazo, Carlos Oscar S Sanchez
Regarding the DeepAlign program, I am not sure if it has been included
in this release. Probably Pablo, Grigory, or Alberto can give us more
details about the availability of this program in Scipion.
Kind regards,
David Herreros
|
1 message has been excluded from this view by a project administrator.
