Process terminated with an error exit status (127)

1

Hello,

I’m running TractoFlow 2.4.3 with NextFlow 21.04.0 on Ubuntu 22.04, and I’m getting Process terminated with an error exit status (127) errors:

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The command of each process doesn’t seem to be recognized — I checked the .command.err log files, and they have the command not found error. Could you help me understand this problem?

Thank you,
Beatriz

2

Hello @beatrizcepa,

Can you send me the command line you run ?

Thanks
Arnaud

3

Hi @abore

I’m running this command NXF_VER=21.04.0 nextflow run tractoflow -r 2.4.3 --input=/home/ubuntu/mri/ --run_pft_tracking=false --pft_compress_streamlines=false --local_compress_streamlines=false .

Beatriz

4

You forgot to include the singularity. Please add -with-singularity PATH_TO_THE_SIF_FILE
You can download it from here

Check this link

Hope it helps

Best,
Arnaud

5

It doesn’t solve the problem. Can it be because I installed TractoFlow with nextflow pull scilus/tractoflow instead of downloading the singularity container?

Thanks,
Beatriz

6

If you are using docker the link I sent you gives you an idea of what your command line should look like.

I put it back here

Arnaud

7

sorry I read your message too fast.

Tractoflow needs a container to run with.
Using nextflow pull you downloaded the software but it needs the whole environment to work with. You can use singularity or docker, either way you choose is described in the documentation.

Don’t hesitate if you have more questions.
Arnaud

8

Oh okay, I’ll do that then. Thank you!

Beatriz