Terminated with error but no error message in the log

1

Hi
I am running tractoflow pipeline with docker in macOS 14.1.2 as:

nextflow run tractoflow -r 2.4.2 --bids bids -with-docker scilus/scilus:1.5.0

The run stops after denoising with following:

[a5/ea15c1] NOTE: Process `Eddy (sub-001_ses-03_run-1)` terminated with an error exit status (1) -- Execution is retried (1)
[6f/6fd618] NOTE: Process `Eddy (sub-001_ses-03_run-1)` terminated with an error exit status (1) -- Execution is retried (1)
[45/23d05a] NOTE: Process `Eddy (sub-001_ses-03_run-1)` terminated with an error exit status (1) -- Execution is retried (2)
[cf/d37918] NOTE: Process `Eddy (sub-001_ses-03_run-1)` terminated with an error exit status (1) -- Execution is retried (2)
[0f/b65ee7] NOTE: Process `Eddy (sub-001_ses-03_run-1)` terminated with an error exit status (1) -- Execution is retried (1)
[21/a3e1a0] NOTE: Process `Eddy (sub-001_ses-03_run-1)` terminated with an error exit status (1) -- Execution is retried (3)
[de/18d1e6] NOTE: Process `Eddy (sub-001_ses-03_run-1)` terminated with an error exit status (1) -- Execution is retried (3)
[fe/c9533b] NOTE: Process `Eddy (sub-001_ses-03_run-1)` terminated with an error exit status (1) -- Execution is retried (2)
[00/e83a17] NOTE: Process `Eddy (sub-001_ses-03_run-1)` terminated with an error exit status (1) -- Error is ignored
[7b/d966bf] NOTE: Process `Eddy (sub-001_ses-03_run-1)` terminated with an error exit status (1) -- Error is ignored
[e0/16130c] NOTE: Process `Eddy (sub-001_ses-03_run-1)` terminated with an error exit status (1) -- Execution is retried (3)
[7d/86401f] NOTE: Process `Eddy (sub-001_ses-03_run-1)` terminated with an error exit status (1) -- Error is ignored
Completed at: 05-Dec-2023 09:42:20
Duration    : 1m 27s
CPU hours   : 0.1 (10.4% failed)
Succeeded   : 8
Ignored     : 4
Failed      : 16

When I check the logs I don’t see an error to resolve, just a warning:

WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

Any Suggestions on how to proceed?

Thanks

2

Dear @Akram,

Sorry for the delay, can you show what’s inside work/a5/ea15c1*/.command.err ?

Thank you
Arnaud

3

@abore Thank you for getting back to me.

I ran it again with
nextflow run tractoflow -r 2.4.2 --bids bids -profile macos -with-docker scilus/scilus:1.5.0 -resume

The first error happens as below:
[0d/2aa195] NOTE: Process N4_T1 (sub-001_ses-03_run-1) terminated with an error exit status (132) -- Execution is retried (1)

and in the error message is:
work/0d/2aa1955cb366568e4854a404a29d77/.command.sh: line 5: 35 Illegal instruction N4BiasFieldCorrection -i sub-001_ses-03_run-01_T1w.nii.gz -o [sub-001_ses-03_run-1__t1_n4.nii.gz, bias_field_t1.nii.gz] -c [300x150x75x50, 1e-6] -v 1

4

Hi @Akram,

I’m a little bit confused the first message you sent me showed errors in the Eddy process and now it’s N4.
What is the first failing process ? Then send me these files: command.sh, command.err and command.log et finally if you can run a mrinfo, fslinfo or scil_print_header.py on the input file of this command that would be very helpful.

Also, I highly suggest you to run the latest version of tractoflow 2.4.3 combined with the latest container scilus_1.6.0.sif

Thank you
Arnaud

5

Hi @abore
The first error occurs with N4 as far as I see. I ran the latest version as you advised:

nextflow run tractoflow -r 2.4.3 --bids bids -profile macos -with-docker scilus/scilus:1.6.0

Error folder

Here is fslinfo output on the input of the command:

fslinfo sub-001_ses-03_run-01_T1w.nii.gz
data_type	INT16
dim1		192
dim2		240
dim3		256
dim4		1
datatype	4
pixdim1		1.000000
pixdim2		1.000000
pixdim3		1.000000
pixdim4		2.300000
cal_max		0.000000
cal_min		0.000000
file_type	NIFTI-1+

Thank you,
Akram

6

Hi @Akram ,

It seems to be an issue with the way we built ANTs in the docker. When used with old CPU it may not work. See this discussion. We are currently testing it and I’ll let you now asap. Sorry for the delay.

Best,
Arnaud

7

Hi @abore,

Thanks for getting back to me. As I read the discussion you pointed out that one thing remains unclear. My CPU is M1 Pro so not old. Also, I chose the “Use Rosetta for x86/amd64 emulation on Apple Silicon” option in my docker if it could be helpful. Could the source of the problem be somewhere else?

Thank you,
Akram

8

Hi @Akram ,

Just read your answer and I’m now confused…
Anyway we now have a new version of the docker scilus/scilus:1.6.0.
We kept exactly the same name since it should not change anything.

Can you give it a try ?

Best,
Arnaud

9

Hi @abore,

I appreciate your help. I pulled the docker update and the pipeline was completed successfully.

Best,
Akram

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