Fmriprep killed during autorecon_surfs0

Hi Neurostars,

I ran #fmriprep (v 21.0.2) successfully on my dataset, except for one subject.
The job has been hanging for several days (about 4-5 days) and was eventually killed.
No errors are printed in the log. Running the job with increased verbosity did not help.
Please find the last lines of the log below (please note that it took 3 days to finish #autorecon_surfs1).
Could you help me understand what went wrong?

Thank you!

220606-16:31:41,570 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 226.22/226.22, Free processors: 40/40.
220606-16:31:43,569 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 226.22/226.22, Free processors: 40/40.
220606-16:31:43,777 nipype.workflow INFO:
[Node] Setting-up “_autorecon_surfs0” in “/home/k2148437/arts/work/sub-057/fmriprep_wf/single_subject_057_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0”.
220606-16:31:43,778 nipype.workflow INFO:
[Node] Setting-up “_autorecon_surfs1” in “/home/k2148437/arts/work/sub-057/fmriprep_wf/single_subject_057_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1”.
220606-16:31:43,788 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-057 -sd /home/k2148437/arts/output/sub-057/sourcedata/freesurfer
220606-16:31:43,789 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-057 -sd /home/k2148437/arts/output/sub-057/sourcedata/freesurfer
220606-16:31:43,789 nipype.workflow INFO:
[Node] Running “_autorecon_surfs0” (“smriprep.interfaces.freesurfer.ReconAll”), a CommandLine Interface with command:
recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-057 -sd /home/k2148437/arts/output/sub-057/sourcedata/freesurfer
220606-16:31:43,790 nipype.workflow INFO:
[Node] Running “_autorecon_surfs1” (“smriprep.interfaces.freesurfer.ReconAll”), a CommandLine Interface with command:
recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-057 -sd /home/k2148437/arts/output/sub-057/sourcedata/freesurfer
220606-16:31:43,791 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-057 -sd /home/k2148437/arts/output/sub-057/sourcedata/freesurfer
220606-16:31:43,791 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-057 -sd /home/k2148437/arts/output/sub-057/sourcedata/freesurfer
220606-16:31:45,570 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 216.22/226.22, Free processors: 24/40.
Currently running:
* _autorecon_surfs1
* _autorecon_surfs0
220609-09:03:36,549 nipype.workflow INFO:
[Node] Finished “_autorecon_surfs1”.
220609-09:03:38,469 nipype.workflow INFO:
[Job 2020] Completed (_autorecon_surfs1).
220609-09:03:38,474 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 221.22/226.22, Free processors: 32/40.
Currently running:
* _autorecon_surfs0

Can you check the FreeSurfer logs? They’ll be found in the <freesurfer-dir>/sub-057/scripts/*.log.

Thank you effigies.
Turns out the job was killed due to a problem on our server.
It has finished successfully now.