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Re: [scipion-users] FAILED substractStep when testing localized reconstruction tutorial
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From: Roberto M. <ro...@cn...> - 2022-02-04 22:01:14
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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
>
>
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