/dev/fd/63: line 1: 404:: command not found

[wilfriedguiblet]

Howdy,

I got this error running the test files as described in the tutorial. Any idea what's wrong?

####################################################################################################
Tet1n2DKOalkBtRNA
2
WTtRNA
2
# Pipeline Parameters:
####################################################################################################
# Working dir : /scratch/cluster_scratch/$USER/TRANQUIL_test
# Results dir : /scratch/cluster_scratch/$USER/TRANQUIL_test/results
# Scripts dir : /scratch/cluster_scratch/$USER/TRANQUIL_test/scripts
# Resources dir : /scratch/cluster_scratch/$USER/TRANQUIL_test/resources
# Cluster JSON : /scratch/cluster_scratch/$USER/TRANQUIL_test/resources/cluster.json
/dev/fd/63: line 1: 404:: command not found

Thanks!

[kelly-sovacool]

Hi Wilfried, I'm confused by this error because I'm not able to reproduce it and we have other collaborators who do not encounter it.

Can you confirm that you're running commands like this?

/mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL/tranquil -w=/scratch/cluster_scratch/$USER/tranquil_test_2025-06-12 -m=init
/mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL/tranquil -w=/scratch/cluster_scratch/$USER/tranquil_test_2025-06-12 -m=dryrun
/mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL/tranquil -w=/scratch/cluster_scratch/$USER/tranquil_test_2025-06-12 -m=run

(p.s. there is a problem with the test dataset, later on during the mimseq job it will fail during deseq2 -- but you should be able to get at least to that step with this dataset)

[kelly-sovacool]

@wilfriedguiblet can you try the tranquil version here? /mnt/projects/CCBR-Pipelines/Pipelines/TRANQUIL/v0.3/tranquil