77 lines
48 KiB
(Stored with Git Annex)
Text
77 lines
48 KiB
(Stored with Git Annex)
Text
+ dssource=ria+file:///data/project/QC_workflow/TMP/RIA_QCworkflow/inputstore#2d58dd48-4166-4dc3-9cd1-64f3d0665a8c
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+ pushgitremote=file:///data/project/QC_workflow/TMP/RIA_QCworkflow/2d5/8dd48-4166-4dc3-9cd1-64f3d0665a8c
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+ subid=sub-0001
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+ export 'DUCT_OUTPUT_PREFIX=logs/duct/sub-0001_{datetime_filesafe}-{pid}_'
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+ DUCT_OUTPUT_PREFIX='logs/duct/sub-0001_{datetime_filesafe}-{pid}_'
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+ datalad clone ria+file:///data/project/QC_workflow/TMP/RIA_QCworkflow/inputstore#2d58dd48-4166-4dc3-9cd1-64f3d0665a8c ds
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[INFO] Attempting a clone into /var/lib/condor/execute/dir_3279331/ds
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[INFO] Attempting to clone from file:///data/project/QC_workflow/TMP/RIA_QCworkflow/inputstore/2d5/8dd48-4166-4dc3-9cd1-64f3d0665a8c to /var/lib/condor/execute/dir_3279331/ds
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[INFO] Completed clone attempts for Dataset(/var/lib/condor/execute/dir_3279331/ds)
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+ cd ds
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+ git remote add outputstore file:///data/project/QC_workflow/TMP/RIA_QCworkflow/2d5/8dd48-4166-4dc3-9cd1-64f3d0665a8c
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+ git checkout -b job_sub-0001_9220573
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Switched to a new branch 'job_sub-0001_9220573'
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+ datalad get -n sourcedata/raw/
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[INFO] Attempting a clone into /var/lib/condor/execute/dir_3279331/ds/sourcedata/raw
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[INFO] Attempting to clone from file:///data/project/QC_workflow/TMP/RIA_QCworkflow/inputstore/2ee/2bfa7-6c1b-4cf6-87e9-297e30f42517 to /var/lib/condor/execute/dir_3279331/ds/sourcedata/raw
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[INFO] Attempting to clone from https://github.com/OpenNeuroDatasets/ds005256.git to /var/lib/condor/execute/dir_3279331/ds/sourcedata/raw
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[INFO] Start enumerating objects
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[INFO] Start receiving objects
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[INFO] Start resolving deltas
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[INFO] Completed clone attempts for Dataset(/var/lib/condor/execute/dir_3279331/ds/sourcedata/raw)
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[INFO] Remote origin not usable by git-annex; setting annex-ignore
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[INFO] https://github.com/OpenNeuroDatasets/ds005256.git/config download failed: Not Found
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[INFO] access to 1 dataset sibling openneuro not auto-enabled, enable with:
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| datalad siblings -d "/var/lib/condor/execute/dir_3279331/ds/sourcedata/raw" enable -s openneuro
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+ datalad containers-run -m 'Compute MRIQC for sub-0001' -n bids-mriqc -i sourcedata/raw/sub-0001 -i sourcedata/raw/dataset_description.json mriqc sourcedata/raw . participant --participant-label sub-0001 --no-datalad-get --no-sub --verbose --nprocs 1 --mem 3000 --work-dir /tmp --float32 --verbose-reports
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[INFO] Making sure inputs are available (this may take some time)
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[INFO] Attempting a clone into /var/lib/condor/execute/dir_3279331/ds/code/containers
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[INFO] Attempting to clone from file:///data/project/QC_workflow/TMP/RIA_QCworkflow/inputstore/b02/e63c2-62c1-11e9-82b0-52540040489c to /var/lib/condor/execute/dir_3279331/ds/code/containers
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[INFO] Attempting to clone from https://github.com/ReproNim/containers.git to /var/lib/condor/execute/dir_3279331/ds/code/containers
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[INFO] Start enumerating objects
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[INFO] Start counting objects
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[INFO] Start compressing objects
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[INFO] Start receiving objects
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[INFO] Start resolving deltas
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[INFO] Completed clone attempts for Dataset(/var/lib/condor/execute/dir_3279331/ds/code/containers)
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[INFO] Remote origin not usable by git-annex; setting annex-ignore
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[INFO] https://github.com/ReproNim/containers.git/config download failed: Not Found
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[INFO] == Command start (output follows) =====
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2025-09-17T23:06:15+0200 [INFO ] con-duct: duct 0.16.0 is executing 'singularity exec -W /tmp/singtmp.Bd9f5Y -B /var/lib/condor/execute/dir_3279331/ds/code/containers/binds/zoneinfo/UTC:/etc/localtime -B /tmp/singtmp.Bd9f5Y/tmp:/tmp -B /tmp/singtmp.Bd9f5Y/var/tmp:/var/tmp -e -B /var/lib/condor/execute/dir_3279331/ds -H /var/lib/condor/execute/dir_3279331/ds/code/containers/binds/HOME --pwd /var/lib/condor/execute/dir_3279331/ds code/containers/images/bids/bids-mriqc--24.0.2.sing mriqc sourcedata/raw . participant --participant-label sub-0001 --no-datalad-get --no-sub --verbose --nprocs 1 --mem 3000 --work-dir /tmp --float32 --verbose-reports'...
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2025-09-17T23:06:15+0200 [INFO ] con-duct: Log files will be written to logs/duct/sub-0001_2025.09.17T23.06.15-3344424_
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Fontconfig error: No writable cache directories
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Fontconfig error: No writable cache directories
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Fontconfig error: No writable cache directories
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Fontconfig error: No writable cache directories
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Fontconfig error: No writable cache directories
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Fontconfig error: No writable cache directories
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Fontconfig error: No writable cache directories
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Fontconfig error: No writable cache directories
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/opt/conda/lib/python3.11/site-packages/nilearn/plotting/displays/_slicers.py:420: UserWarning: empty mask
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xmin_, xmax_, ymin_, ymax_, zmin_, zmax_ = get_mask_bounds(
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2025-09-18T16:08:20+0200 [INFO ] con-duct: Summary:
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Exit Code: 0
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Command: singularity exec -W /tmp/singtmp.Bd9f5Y -B /var/lib/condor/execute/dir_3279331/ds/code/containers/binds/zoneinfo/UTC:/etc/localtime -B /tmp/singtmp.Bd9f5Y/tmp:/tmp -B /tmp/singtmp.Bd9f5Y/var/tmp:/var/tmp -e -B /var/lib/condor/execute/dir_3279331/ds -H /var/lib/condor/execute/dir_3279331/ds/code/containers/binds/HOME --pwd /var/lib/condor/execute/dir_3279331/ds code/containers/images/bids/bids-mriqc--24.0.2.sing mriqc sourcedata/raw . participant --participant-label sub-0001 --no-datalad-get --no-sub --verbose --nprocs 1 --mem 3000 --work-dir /tmp --float32 --verbose-reports
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Log files location: logs/duct/sub-0001_2025.09.17T23.06.15-3344424_
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Wall Clock Time: 61324.997 sec
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Memory Peak Usage (RSS): 11.5 GB
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Memory Average Usage (RSS): 2.0 GB
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Virtual Memory Peak Usage (VSZ): 16.9 GB
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Virtual Memory Average Usage (VSZ): 4.7 GB
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Memory Peak Percentage: 2.00%
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Memory Average Percentage: 0.23%
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CPU Peak Usage: 220.00%
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Average CPU Usage: 90.67%
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[INFO] == Command exit (modification check follows) =====
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+ datalad push --to mriqc_out-storage
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[INFO] Determine push target
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[INFO] Push refspecs
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[INFO] Transfer data
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[INFO] Finished push of Dataset(/var/lib/condor/execute/dir_3279331/ds)
|
|
+ flock --verbose /data/project/QC_workflow/TMP/ds005256-mriqc/.condor_datalad_lock git push outputstore
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|
To file:///data/project/QC_workflow/TMP/RIA_QCworkflow/2d5/8dd48-4166-4dc3-9cd1-64f3d0665a8c
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|
* [new branch] job_sub-0001_9220573 -> job_sub-0001_9220573
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|
+ echo SUCCESS
|