Dear NeuroStar members,
I’m running tractoflow in Ubuntu 20.04.0 and I’m getting an error
caused by falling to pull singularity image.
Code to run:
nextflow run /home/eduardo/tractoflow-2.1.1/main.nf --root Tractoflow/ --dti_shells “0 1000” --fodf_shells “0 1000” -with-singularity tractoflow_2.1.1_650f776_2020-07-15.img
Output:
N E X T F L O W ~ version 20.10.0
Launching /home/eduardo/tractoflow-2.1.1/main.nf [pedantic_volta] - revision: d21c9a89e5
TractoFlow pipeline
Start time: 2021-02-19T16:53:15.244486-02:00
[Git Info]
null - null [null]
Options
[Denoise DWI]
Denoise DWI: true
[Topup]
Run Topup: true
[Eddy]
Run Eddy: true
Eddy command: eddy_openmp
[Resample DWI]
Resample DWI: true
Resolution: 1
[DTI shells]
DTI shells: 0 1000
[fODF shells]
fODF shells: 0 1000
[Compute fiber response function (FRF)]
Set FRF: false
FRF value: 15,4,4
[Mean FRF]
Mean FRF: true
[FODF Metrics]
FODF basis: descoteaux07
SH order: 8
[Seeding mask]
WM seeding: true
[PFT tracking]
Algo: prob
Seeding type: npv
Number of seeds: 10
Random seed: 0
Step size: 0.5
Theta: 20
Minimum length: 20
Maximum length: 200
FODF basis: descoteaux07
Compress streamlines: true
Compressing threshold: 0.2
Number of processes per tasks
T1 brain extraction: 4
Denoise DWI: 4
Denoise T1: 4
Eddy: 1
Compute fODF: 4
Registration: 4
Template T1 path
Template T1: /human-data/mni_152_sym_09c/t1
Input: Tractoflow/
[- ] process > README -
[- ] process > Bet_Prelim_DWI -
[- ] process > Denoise_DWI -
[- ] process > Topup -
[- ] process > Eddy -
[- ] process > Eddy_Topup -
[- ] process > README -
[- ] process > Bet_Prelim_DWI -
[- ] process > Denoise_DWI -
[- ] process > Topup -
[- ] process > Eddy -
[- ] process > Eddy_Topup -
[- ] process > Extract_B0 -
[- ] process > Bet_DWI -
[- ] process > N4_DWI -
[- ] process > Crop_DWI -
[- ] process > Denoise_T1 -
[- ] process > N4_T1 -
[- ] process > Resample_T1 -
[- ] process > Bet_T1 -
[- ] process > README -
[- ] process > Bet_Prelim_DWI -
[- ] process > Denoise_DWI -
[- ] process > Topup -
[- ] process > Eddy -
[- ] process > Eddy_Topup -
[- ] process > Extract_B0 -
[- ] process > Bet_DWI -
[- ] process > N4_DWI -
[- ] process > Crop_DWI -
[- ] process > Denoise_T1 -
[- ] process > N4_T1 -
[- ] process > Resample_T1 -
[- ] process > Bet_T1 -
[- ] process > Crop_T1 -
[- ] process > Normalize_DWI -
[- ] process > Resample_DWI -
[- ] process > Resample_B0 -
[- ] process > Extract_DTI_Shell -
[- ] process > DTI_Metrics -
[- ] process > Extract_FODF_Shell -
[- ] process > Register_T1 -
[- ] process > Segment_Tissues -
[- ] process > Compute_FRF -
[- ] process > Mean_FRF -
[- ] process > FODF_Metrics -
[- ] process > PFT_Maps -
[- ] process > Seeding_Mask -
[- ] process > Tracking -
Pulling Singularity image docker://tractoflow_2.1.1_650f776_2020-07-15.img [cache /home/eduardo/Area_de_trabalho/Grant_Tractography/work/singularity/tractoflow_2.1.1_650f776_2020-07-15.img.img]
[- ] process > README -
[- ] process > Bet_Prelim_DWI -
[- ] process > Denoise_DWI -
[- ] process > Topup -
[- ] process > Eddy -
[- ] process > Eddy_Topup -
[- ] process > Extract_B0 -
[- ] process > Bet_DWI -
[- ] process > N4_DWI -
[- ] process > Crop_DWI -
[- ] process > Denoise_T1 -
[- ] process > N4_T1 -
[- ] process > Resample_T1 -
[- ] process > Bet_T1 -
[- ] process > Crop_T1 -
[- ] process > Normalize_DWI -
[- ] process > Resample_DWI -
[- ] process > Resample_B0 -
[- ] process > Extract_DTI_Shell -
[- ] process > DTI_Metrics -
[- ] process > Extract_FODF_Shell -
[- ] process > Register_T1 -
[- ] process > Segment_Tissues -
[- ] process > Compute_FRF -
[- ] process > Mean_FRF -
[- ] process > FODF_Metrics -
[- ] process > PFT_Maps -
[- ] process > Seeding_Mask -
[- ] process > Tracking -
Pulling Singularity image docker://tractoflow_2.1.1_650f776_2020-07-15.img [cache /home/eduardo/Area_de_trabalho/Grant_Tractography/work/singularity/tractoflow_2.1.1_650f776_2020-07-15.img.img]
WARN: Singularity cache directory has not been defined – Remote image will be stored in the path: /home/eduardo/Area_de_trabalho/Grant_Tractography/work/singularity – Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
Error executing process > ‘Bet_Prelim_DWI (S1)’
Caused by:
Failed to pull singularity image
command: singularity pull --name tractoflow_2.1.1_650f776_2020-07-15.img.img.pulling.1613760797920 docker://tractoflow_2.1.1_650f776_2020-07-15.img > /dev/null
status : 1
message:
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
ERROR UNAUTHORIZED: authentication required
ERROR Check existence, naming, and permissions
ERROR: pulling container failed!
Please, I would appreciate if anybody could help me with this issue.
Sincerely,
Eduardo