change rule structure so synthsr only clones once

[mackenziesnyder]

• create synthsr.smk file
• created rule so synthsr only clones once
• tested with multiple subjects
• for Error in SynthSR Step with git clone being parallelized  #61

[ataha24]

@mackenziesnyder amazing work as always! Just tested this and a couple of errors to point out:

Select jobs to execute... [UserWarning] /home/UWO/ataha24/miniconda3/envs/autoafids-dev/lib/python3.10/site-packages/stopit/__init__.py:10 import pkg_resources pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.

ERROR:root:Error running SynthSR: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-04/ses-1/anat/sub-04_ses-1_T2w.nii.gz', 'work/sub-04/ses-1/SynthSR/sub-04_ses-1_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. Traceback (most recent call last): File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmpp2r1o5he.run_synthsr.py", line 47, in <module> ERROR:root:Error running SynthSR: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-09/ses-1/anat/sub-09_ses-1_T2w.nii.gz', 'work/sub-09/ses-1/SynthSR/sub-09_ses-1_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. ERROR:root:Error running SynthSR: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-06/ses-1/anat/sub-06_ses-1_T2w.nii.gz', 'work/sub-06/ses-1/SynthSR/sub-06_ses-1_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. run_program( File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmpp2r1o5he.run_synthsr.py", line 30, in run_program subprocess.run( File "/localscratch/.cache/autoafids/conda/87c75fce25d462448de2c063b011cbc6_/lib/python3.8/subprocess.py", line 516, in run Traceback (most recent call last): File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmp93cdjf20.run_synthsr.py", line 47, in <module> Traceback (most recent call last): File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmpq9dpbys2.run_synthsr.py", line 47, in <module> raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-04/ses-1/anat/sub-04_ses-1_T2w.nii.gz', 'work/sub-04/ses-1/SynthSR/sub-04_ses-1_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. run_program( File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmp93cdjf20.run_synthsr.py", line 30, in run_program run_program( subprocess.run( File "/localscratch/.cache/autoafids/conda/87c75fce25d462448de2c063b011cbc6_/lib/python3.8/subprocess.py", line 516, in run File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmpq9dpbys2.run_synthsr.py", line 30, in run_program subprocess.run( raise CalledProcessError(retcode, process.args, File "/localscratch/.cache/autoafids/conda/87c75fce25d462448de2c063b011cbc6_/lib/python3.8/subprocess.py", line 516, in run subprocess.CalledProcessError: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-09/ses-1/anat/sub-09_ses-1_T2w.nii.gz', 'work/sub-09/ses-1/SynthSR/sub-09_ses-1_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-06/ses-1/anat/sub-06_ses-1_T2w.nii.gz', 'work/sub-06/ses-1/SynthSR/sub-06_ses-1_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. ERROR:root:Error running SynthSR: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-02/ses-2/anat/sub-02_ses-2_T2w.nii.gz', 'work/sub-02/ses-2/SynthSR/sub-02_ses-2_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. Traceback (most recent call last): File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmp76in32r0.run_synthsr.py", line 47, in <module> run_program( File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmp76in32r0.run_synthsr.py", line 30, in run_program subprocess.run( File "/localscratch/.cache/autoafids/conda/87c75fce25d462448de2c063b011cbc6_/lib/python3.8/subprocess.py", line 516, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-02/ses-2/anat/sub-02_ses-2_T2w.nii.gz', 'work/sub-02/ses-2/SynthSR/sub-02_ses-2_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1.

[ataha24]

@mackenziesnyder amazing work as always! Just tested this and a couple of errors to point out:

Select jobs to execute... [UserWarning] /home/UWO/ataha24/miniconda3/envs/autoafids-dev/lib/python3.10/site-packages/stopit/__init__.py:10 import pkg_resources pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.

ERROR:root:Error running SynthSR: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-04/ses-1/anat/sub-04_ses-1_T2w.nii.gz', 'work/sub-04/ses-1/SynthSR/sub-04_ses-1_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. Traceback (most recent call last): File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmpp2r1o5he.run_synthsr.py", line 47, in <module> ERROR:root:Error running SynthSR: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-09/ses-1/anat/sub-09_ses-1_T2w.nii.gz', 'work/sub-09/ses-1/SynthSR/sub-09_ses-1_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. ERROR:root:Error running SynthSR: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-06/ses-1/anat/sub-06_ses-1_T2w.nii.gz', 'work/sub-06/ses-1/SynthSR/sub-06_ses-1_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. run_program( File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmpp2r1o5he.run_synthsr.py", line 30, in run_program subprocess.run( File "/localscratch/.cache/autoafids/conda/87c75fce25d462448de2c063b011cbc6_/lib/python3.8/subprocess.py", line 516, in run Traceback (most recent call last): File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmp93cdjf20.run_synthsr.py", line 47, in <module> Traceback (most recent call last): File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmpq9dpbys2.run_synthsr.py", line 47, in <module> raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-04/ses-1/anat/sub-04_ses-1_T2w.nii.gz', 'work/sub-04/ses-1/SynthSR/sub-04_ses-1_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. run_program( File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmp93cdjf20.run_synthsr.py", line 30, in run_program run_program( subprocess.run( File "/localscratch/.cache/autoafids/conda/87c75fce25d462448de2c063b011cbc6_/lib/python3.8/subprocess.py", line 516, in run File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmpq9dpbys2.run_synthsr.py", line 30, in run_program subprocess.run( raise CalledProcessError(retcode, process.args, File "/localscratch/.cache/autoafids/conda/87c75fce25d462448de2c063b011cbc6_/lib/python3.8/subprocess.py", line 516, in run subprocess.CalledProcessError: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-09/ses-1/anat/sub-09_ses-1_T2w.nii.gz', 'work/sub-09/ses-1/SynthSR/sub-09_ses-1_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-06/ses-1/anat/sub-06_ses-1_T2w.nii.gz', 'work/sub-06/ses-1/SynthSR/sub-06_ses-1_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. ERROR:root:Error running SynthSR: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-02/ses-2/anat/sub-02_ses-2_T2w.nii.gz', 'work/sub-02/ses-2/SynthSR/sub-02_ses-2_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1. Traceback (most recent call last): File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmp76in32r0.run_synthsr.py", line 47, in <module> run_program( File "/home/UWO/ataha24/Desktop/377T_TEST/.snakemake/scripts/tmp76in32r0.run_synthsr.py", line 30, in run_program subprocess.run( File "/localscratch/.cache/autoafids/conda/87c75fce25d462448de2c063b011cbc6_/lib/python3.8/subprocess.py", line 516, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['python', '/localscratch/.cache/autoafids/SynthSR/scripts/predict_command_line.py', '/home/UWO/ataha24/graham/projects/ctb-akhanf/ataha24/0.afids_data/datalad/afids-data/data/datasets/3T7T/sub-02/ses-2/anat/sub-02_ses-2_T2w.nii.gz', 'work/sub-02/ses-2/SynthSR/sub-02_ses-2_desc-T2w-SynthSR_T1w.nii.gz', '--cpu']' returned non-zero exit status 1.

I am not sure if the second one is because how I have set up miniconda on my CBS so would defer to @Dhananjhay to see if he comes across this.

[Dhananjhay]

Hey guys! Sorry for the delay; it was a little tricky to upload SynthSR's conda package but its finally done, and we don't have to change the schema anymore. I'm running autoafids with the SynthSR conda package for 87 subjects and I haven't ran into memory or git issues till now. You can test these new changes in the PR #76.

[mackenziesnyder]

Hey guys! Sorry for the delay; it was a little tricky to upload SynthSR's conda package but its finally done, and we don't have to change the schema anymore. I'm running autoafids with the SynthSR conda package for 87 subjects and I haven't ran into memory or git issues till now. You can test these new changes in the PR #76.

Sounds good - I will test it out!