91 lines
6.2 KiB
Text
91 lines
6.2 KiB
Text
+ dssource=ria+file:///data/project/QC_workflow/TMP/RIA_QCworkflow/inputstore#90150bd5-f30d-466d-bc02-120014a29d33
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+ pushgitremote=file:///data/project/QC_workflow/TMP/RIA_QCworkflow/901/50bd5-f30d-466d-bc02-120014a29d33
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+ subd=sub-802945
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++ basename sub-802945
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+ subid=sub-802945
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+ datalad clone ria+file:///data/project/QC_workflow/TMP/RIA_QCworkflow/inputstore#90150bd5-f30d-466d-bc02-120014a29d33 ds
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[INFO] Attempting a clone into /var/lib/condor/execute/dir_922560/ds
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[INFO] Attempting to clone from file:///data/project/QC_workflow/TMP/RIA_QCworkflow/inputstore/901/50bd5-f30d-466d-bc02-120014a29d33 to /var/lib/condor/execute/dir_922560/ds
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[INFO] Completed clone attempts for Dataset(/var/lib/condor/execute/dir_922560/ds)
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+ cd ds
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+ git remote add outputstore file:///data/project/QC_workflow/TMP/RIA_QCworkflow/901/50bd5-f30d-466d-bc02-120014a29d33
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+ git checkout -b job-sub-802945.10071039
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Switched to a new branch 'job-sub-802945.10071039'
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+ datalad get -n sourcedata/raw/
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[INFO] Attempting a clone into /var/lib/condor/execute/dir_922560/ds/sourcedata/raw
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[INFO] Attempting to clone from file:///data/project/QC_workflow/TMP/RIA_QCworkflow/inputstore/ed5/5652a-f57e-4c7f-b519-84735d016b83 to /var/lib/condor/execute/dir_922560/ds/sourcedata/raw
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[INFO] Attempting to clone from https://github.com/OpenNeuroDatasets/ds004173.git to /var/lib/condor/execute/dir_922560/ds/sourcedata/raw
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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_922560/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/ds004173.git/config download failed: Not Found
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+ find sourcedata/raw/sub-802945 -name 'sub-802945*T1w.nii.gz' -exec sh -c '
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odir=$(echo {} | cut -d / -f3);
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datalad containers-run \
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-m "Compute CAT12.9 QC for $odir" \
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-n cat12-9\
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--explicit \
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-o $odir \
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-i {} \
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sh -e -u -x -c "
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mkdir -p {outputs[0]} || true \
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&& cp {inputs[0]} {outputs[0]} \
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&& /singularity -b /batch/CATpreprocessing4qc+ROIs.m {outputs[0]}/*.nii.gz \
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&& rm -f {outputs[0]}/*.nii* {outputs[0]}/report/*.jpg \
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&& gzip {outputs[0]}/*/*.nii \
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" \
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' ';'
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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_922560/ds/code/cat12
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[INFO] Attempting to clone from file:///data/project/QC_workflow/TMP/RIA_QCworkflow/inputstore/03b/35ee0-e4d6-4363-9288-86b835e98525 to /var/lib/condor/execute/dir_922560/ds/code/cat12
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[INFO] Attempting to clone from file:///data/project/cat_preprocessed/dataladstore/alias/cat12.9 to /var/lib/condor/execute/dir_922560/ds/code/cat12
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[INFO] Completed clone attempts for Dataset(/var/lib/condor/execute/dir_922560/ds/code/cat12)
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[INFO] Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
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| BrokenPipeError: [Errno 32] Broken pipe
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[INFO] Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
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| BrokenPipeError: [Errno 32] Broken pipe
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| Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
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| BrokenPipeError: [Errno 32] Broken pipe
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[WARNING] Found multiple matching ORA remotes. Couldn't decide which one publishing to 'origin' should depend on: ['inm7-storage', 'juseless-storage']. Consider running 'datalad siblings configure -s origin --publish-depends ORAREMOTENAME' to set publication dependency manually.
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[INFO] == Command start (output follows) =====
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+ mkdir -p sub-802945
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+ cp sourcedata/raw/sub-802945/anat/sub-802945_acq-headmotion1_T1w.nii.gz sub-802945
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+ /singularity -b /batch/CATpreprocessing4qc+ROIs.m sub-802945/sub-802945_acq-headmotion1_T1w.nii.gz
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+ rm -f sub-802945/sub-802945_acq-headmotion1_T1w.nii.gz sub-802945/report/catreportj_sub-802945_acq-headmotion1_T1w.jpg
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+ gzip sub-802945/mri/m0wp1sub-802945_acq-headmotion1_T1w.nii sub-802945/mri/mwp1sub-802945_acq-headmotion1_T1w.nii sub-802945/mri/p0sub-802945_acq-headmotion1_T1w.nii sub-802945/mri/wp0sub-802945_acq-headmotion1_T1w.nii
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[INFO] == Command exit (modification check follows) =====
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[INFO] Making sure inputs are available (this may take some time)
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[INFO] Unlocking files
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[INFO] Recording unlocked state in git
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[INFO] Completed unlocking files
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[INFO] == Command start (output follows) =====
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+ mkdir -p sub-802945
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+ cp sourcedata/raw/sub-802945/anat/sub-802945_acq-standard_T1w.nii.gz sub-802945
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+ /singularity -b /batch/CATpreprocessing4qc+ROIs.m sub-802945/sub-802945_acq-standard_T1w.nii.gz
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+ rm -f sub-802945/sub-802945_acq-standard_T1w.nii.gz sub-802945/report/catreportj_sub-802945_acq-standard_T1w.jpg
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+ gzip sub-802945/mri/m0wp1sub-802945_acq-standard_T1w.nii sub-802945/mri/mwp1sub-802945_acq-standard_T1w.nii sub-802945/mri/p0sub-802945_acq-standard_T1w.nii sub-802945/mri/wp0sub-802945_acq-standard_T1w.nii
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[INFO] == Command exit (modification check follows) =====
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[INFO] Making sure inputs are available (this may take some time)
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[INFO] Unlocking files
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[INFO] Recording unlocked state in git
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[INFO] Completed unlocking files
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[INFO] == Command start (output follows) =====
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+ mkdir -p sub-802945
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+ cp sourcedata/raw/sub-802945/anat/sub-802945_acq-headmotion2_T1w.nii.gz sub-802945
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+ /singularity -b /batch/CATpreprocessing4qc+ROIs.m sub-802945/sub-802945_acq-headmotion2_T1w.nii.gz
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+ rm -f sub-802945/sub-802945_acq-headmotion2_T1w.nii.gz sub-802945/report/catreportj_sub-802945_acq-headmotion2_T1w.jpg
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+ gzip sub-802945/mri/m0wp1sub-802945_acq-headmotion2_T1w.nii sub-802945/mri/mwp1sub-802945_acq-headmotion2_T1w.nii sub-802945/mri/p0sub-802945_acq-headmotion2_T1w.nii sub-802945/mri/wp0sub-802945_acq-headmotion2_T1w.nii
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[INFO] == Command exit (modification check follows) =====
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+ datalad push --to catqc_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_922560/ds)
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+ flock --verbose /data/project/QC_workflow/TMP/ds004173-catqc/.condor_datalad_lock git push outputstore
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To file:///data/project/QC_workflow/TMP/RIA_QCworkflow/901/50bd5-f30d-466d-bc02-120014a29d33
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* [new branch] job-sub-802945.10071039 -> job-sub-802945.10071039
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+ echo SUCCESS
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