[scipion-users] FAILED substractStep when testing localized reconstruction tutorial

[Bing W. <bw...@fs...>]

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