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courtois-neuromod / anat-processing

Pipeline to process anatomical data, including microstructure metrics from DWI and MT data
MIT License
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Missing output #16

Closed jcohenadad closed 3 years ago

jcohenadad commented 3 years ago

working on https://github.com/courtois-neuromod/anat-processing/pull/13

Nextflow complains about:

  Missing output file(s) `sub-01_ses-001_bp-spine_T2w_centerline.nii.gz`

even though the image is output (!)

Terminal output ```console executor > local (4) [cd/b81187] process > T2_Segment_SpinalCord (sub-06_ses-002_rec-dis2d) [ 6%] 1 of 17, failed: 1 [- ] process > publishOutputs - Error executing process > 'T2_Segment_SpinalCord (sub-01_ses-001)' Caused by: Missing output file(s) `sub-01_ses-001_bp-spine_T2w_centerline.nii.gz` expected by process `T2_Segment_SpinalCord (sub-01_ses-001)` Command executed: sct_get_centerline -i sub-01_ses-001_bp-cspine_T2w.nii.gz -c t2 Command exit status: 0 Command output: -- Spinal Cord Toolbox (git-master-0e160998510b22bba054b783eb5fb02bad26bfd8) sct_get_centerline -i sub-01_ses-001_bp-cspine_T2w.nii.gz -c t2 -- Creating temporary folder (/var/folders/s8/4qnm5q1n261ch35b5kkclsb00000gn/T/sct-20210504224045.246460-1zycmto9) Remove temporary files... rm -rf /var/folders/s8/4qnm5q1n261ch35b5kkclsb00000gn/T/sct-20210504224045.246460-1zycmto9 Done! To view results, type: fsleyes sub-01_ses-001_bp-cspine_T2w.nii.gz -cm greyscale sub-01_ses-001_bp-cspine_T2w_centerline.nii.gz -cm red -a 100.0 & Done! To view results, type: fsleyes sub-01_ses-001_bp-cspine_T2w.nii.gz -cm greyscale sub-01_ses-001_bp-cspine_T2w_centerline.nii.gz -cm red -a 70.0 & Work dir: /Users/julien/code/neuromod-anat-processing/work/25/63c5bcbd900a168d6053e11c2e9efe Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` ```
jcohenadad commented 3 years ago

More details from the logfile:

May-04 22:40:49.517 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process `T2_Segment_SpinalCord (sub-01_ses-001)` is unable to find [UnixPath]: `/Users/julien/code/neuromod-anat-processing/work/25/63c5bcbd900a168d6053e11c2e9efe/sub-01_ses-001_bp-spine_T2w_centerline.nii.gz` (pattern: `sub-01_ses-001_bp-spine_T2w_centerline.nii.gz`)
May-04 22:40:49.546 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'T2_Segment_SpinalCord (sub-01_ses-001)'

Caused by:
  Missing output file(s) `sub-01_ses-001_bp-spine_T2w_centerline.nii.gz` expected by process `T2_Segment_SpinalCord (sub-01_ses-001)`
jcohenadad commented 3 years ago

ah! my bad: it was a typo: 

        path("${sid}_bp-spine_T2w_centerline.nii.gz"), \

instead of 

        path("${sid}_bp-cspine_T2w_centerline.nii.gz"), \