C-PAC v1.8.0 dev - Default preconfig

[hahaai]

C-PAC Run Info

Description	replace this with a brief description of your pipeline run
Version	C-PAC v1.8.0 dev
Container	Pulled on 1/21/2021 8:00 PM
System	Upenn Cluster
Data Size	latest 750 volume. 4 HBN CBIC subjects, the same as in the regression test
Results	For CPAC:Default 3 stalls (2 seem finished most of preproc, stall at centrality. ), 1 errored out quickly.

Include:

• [ ] Run Command: .

no pipeline config was specified

• [ ] Pipeline Config (can drag file directly into issue)
• [ ] Data Config (can drag file directly into issue)

Developers only:

• [ ] Default Pipeline Diff:

(print-out from cpac_pipe_diff.py)

• [ ] Screenshots of brain extraction and registration wireframe overlays from QC pages (if available):

screenshots here

• [ ] Node timing information:

(print-out from callback_log_time_parse.py)

• [ ] Extracted time series 1D and nuisance regressors 1D correlations against previous version or some benchmark (can use corr_two_1D.py but heatmaps or other visualizations are good too):

correlations here

[hahaai]

Three subjects were stall. The following are the end of the log:

==> CPAC_out/default_NDARAA947ZG5/log/pipeline_cpac-default-pipeline/sub-NDARAA947ZG5_ses-1/pypeline.log <==
210221-21:50:01,288 nipype.workflow INFO:
     [Node] Finished "cpac_sub-NDARAA947ZG5.nuisance_regressors_default_161.CerebrospinalFluid_mean".
210221-21:50:03,148 nipype.workflow INFO:
     [Job 3688] Completed (cpac_sub-NDARAA947ZG5.nuisance_regressors_default_161.CerebrospinalFluid_mean).
210221-21:50:03,165 nipype.workflow INFO:
     [MultiProc] Running 3 tasks, and 7 jobs ready. Free memory (GB): 9.00/15.00, Free processors: 5/8.
           Currently running:
            * cpac_sub-NDARAA947ZG5.nii_desc-binarized-2_degree-centrality_301
            * cpac_sub-NDARAA947ZG5.nii_desc-binarized-2_eigen-centrality_303
            * cpac_sub-NDARAA947ZG5.nii_desc-binarized-2_lfcd_305

==> CPAC_out/default_NDARAB348EWR/log/pipeline_cpac-default-pipeline/sub-NDARAB348EWR_ses-1/pypeline.log <==
210221-21:31:15,702 nipype.workflow INFO:
     [Node] Finished "cpac_sub-NDARAB348EWR.nuisance_regressors_default_161.CerebrospinalFluid_mean".
210221-21:31:15,911 nipype.workflow INFO:
     [Job 2260] Completed (cpac_sub-NDARAB348EWR.nuisance_regressors_default_161.CerebrospinalFluid_mean).
210221-21:31:15,927 nipype.workflow INFO:
     [MultiProc] Running 3 tasks, and 5 jobs ready. Free memory (GB): 9.00/15.00, Free processors: 5/8.
           Currently running:
            * cpac_sub-NDARAB348EWR.nii_desc-binarized-2_degree-centrality_301
            * cpac_sub-NDARAB348EWR.nii_desc-binarized-2_eigen-centrality_303
            * cpac_sub-NDARAB348EWR.nii_desc-binarized-2_lfcd_305

==> CPAC_out/default_NDARAB458VK9/log/pipeline_cpac-default-pipeline/sub-NDARAB458VK9_ses-1/pypeline.log <==
210221-20:46:06,175 nipype.workflow INFO:
     [MultiProc] Running 7 tasks, and 20 jobs ready. Free memory (GB): 0.00/15.00, Free processors: 1/8.
           Currently running:
            * _func_motion_correct_3dvolreg_967
            * _func_motion_correct_3dvolreg_966
            * cpac_sub-NDARAB458VK9.func_extract_brain_103
            * cpac_sub-NDARAB458VK9.gen_motion_stats_106.cal_DVARS
            * cpac_sub-NDARAB458VK9.segment_74
            * cpac_sub-NDARAB458VK9.func_concat_96
            * cpac_sub-NDARAB458VK9.func_deoblique_93

[hahaai]

For the one stopped early, here is the end of the log. Also no crash file created.

`210221-20:46:20,808 nipype.workflow INFO: [Node] Finished "_func_motion_correct_3dvolreg_964". 210221-20:46:22,383 nipype.workflow INFO: [Job 6018] Completed (_func_motion_correct_3dvolreg_964). 210221-20:46:22,404 nipype.workflow INFO: [MultiProc] Running 6 tasks, and 22 jobs ready. Free memory (GB): 2.00/15.00, Free processors: 2/8. Currently running:

• cpac_sub-NDARAA504CRN.func_extract_brain_103
• cpac_sub-NDARAA504CRN.gen_motion_stats_106.cal_DVARS
• cpac_sub-NDARAA504CRN.segment_74
• _func_motion_correct_3dvolreg_965
• cpac_sub-NDARAA504CRN.func_concat_96
• cpac_sub-NDARAA504CRN.func_deoblique_93 210221-20:46:22,738 nipype.workflow INFO:

Error of subject workflow cpac_sub-NDARAA504CRN

CPAC run error:

Pipeline configuration: cpac-default-pipeline
Subject workflow: cpac_sub-NDARAA504CRN
Elapsed run time (minutes): 13.469686460494994
Timing information saved in /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAA504CRN/log/cpac_individual_timing_cpac-default-pipeline.csv
System time of start:      2021-02-21 20:32:56

210221-20:46:22,740 nipype.workflow WARNING: Excessive usage report failed for /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAA504CRN/log Report generation failed for /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAA504CRN/log NoneType: None `