Error when using tractoflow: Missing output file(s) `readme.txt` expected by process `README (README)`

1

Hi Tractoflow team,
I am using Tractoflow pipeline with Singularity to process DWI data on ComputeCananda.
I could run the pipeline well before via StdEnv/2018.3; however, these days the environment was updated on ComputeCanada (StdEnv/2020), and when I changed to the old environment ( StdEnv/2018.3, also loaded the modules I used before) to test the pipeline, it always gives me the error like that below.

[warm up] executor > local
[ea/30677c] Submitted process > README (README)
[ba/0b01e7] Submitted process > Denoise_T1 (sub-MTL0002)
[53/ae4ffa] Submitted process > Denoise_DWI (sub-MTL0002)
[b7/dd21fb] Submitted process > Bet_Prelim_DWI (sub-MTL0002)
[ea/30677c] NOTE: Missing output file(s) readme.txt expected by process README (README) – Execution is retried (1)
[e6/645b50] Re-submitted process > README (README)
[53/ae4ffa] NOTE: Process Denoise_DWI (sub-MTL0002) terminated with an error exit status (1) – Execution is retried (1)
[60/4e3b16] Re-submitted process > Denoise_DWI (sub-MTL0002)
[b7/dd21fb] NOTE: Process Bet_Prelim_DWI (sub-MTL0002) terminated with an error exit status (2) – Execution is retried (1)
[e6/645b50] NOTE: Missing output file(s) readme.txt expected by process README (README) – Execution is retried (2)
[bc/25bc57] Re-submitted process > Bet_Prelim_DWI (sub-MTL0002)
[60/4e3b16] NOTE: Process Denoise_DWI (sub-MTL0002) terminated with an error exit status (1) – Execution is retried (2)
[10/25888d] Re-submitted process > README (README)
…
When I checked the .command.err file in the directory (work/ea/30677c…), it notes like this :
/bin/bash: line 0: cd: /localscratch/tingqiu.18443347.0/nxf.YqD8X4egu4: No such file or directory

I don’t know why happens like this, because the pipeline can run successfully in the same way before.

Can you please give me some suggestions about this problem?

Thank you in advance!
Ting

2

Hi @qtalwaysrun,

Could you send me your bash file that you give to sbatch please.

Thanks

Guillaume

3

Hi Guillaume，
Here is the job script:

#!/bin/sh
#SBATCH --job-name=tractoflow-aging
#SBATCH --nodes=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=0
#SBATCH --time=24:00:00
#SBATCH --account=ctb-villens

module --force purge
module load StdEnv/2018.3
module load VilleneuveLab # loads nextflow 19.01.0 and ants/2.2.0

module load java/1.8.0_121
module load singularity
#cd /lustre04/scratch/tingqiu/ting/test1
export NXF_CLUSTER_SEED=$(shuf -i 0-16777216 -n 1)

srun nextflow -c ./singularity.conf run ./tractoflow-aging/main.nf --root /home/tingqiu/projects/ctb-villens/tingqiu/test1/sub --dti_shells “0 1000” --fodf_shells “0 1000” --dwi_interpolation “lin” -with-singularity ./singularity_tractoflow_2019-04-01_8b39aee.img

Thank you very much!
Ting

4

Thanks, I don’t have idea why TractoFlow crash for now. Could you paste here the content of your singularity.conf.

On which server do you try to launch tractoflow-aging and which version of tractoflow aging do you use ? If you don’t know could you create an archive with the code in it ?

Thanks

Guillaume

5

Thank you
Here is the content of singularity.conf :singularity.runOptions="–bind /lustre03/project/6032449/tingqiu/test1/".

I run the pipeline on Beluga.
Yes, I don’t know which version of the tractoflow is, but it should be the old version for the errors I showed above. main.txt (34.2 KB)
I also downloaded the new version from Github, but with the same error output.

Thank you very much!