Open pentamorfico opened 1 year ago
Hey,
you could download the remaining docker/singularity files manually and store them at --cachedir ./singularity_images
I know that's not the convenient solution but the fastest for now.
In a quick google search I found the following:
At the beginning of the pipeline execution, I get an error message such as FATAL: While making image from oci registry: while building SIF from layers: conveyor failed to get: no descriptor found for reference or any other mentioning OCI, SIF or Singularity.
Ensure you have an up-to-date version of Singularity. Otherwise you may need to clean some Singularity directories, the singularity one (where pipeline images are stored) in FA-nf base directory and .singularity in your $HOME directory.
I will install singularity on my workstation and replicate your command and check if I get the same error
Best Mike
Hi Mike!
Thanks you very much for your suppafast reply! Doing it that way, It worked! :smiley:
I noticed now that I was following the instructions for the install in the documentation:
conda create -n wtp nextflow==20.07.01 singularity==3.6.1
conda activate wtp
(wtp) $ nextflow run replikation/What_the_Phage -r v1.2.0 --setup ...
And I needed to change the nexftlow version from 20.07.01 to 21.04. Perhaps singularity also needs to be updated to a more recent version? Could that be the cause of the issue? I can try to replicate the error in a new environment if that helps
Sorry if my previous message sounded a bit rude, I was in a rush :sweat:
thats what this issue section is for :D, also I want to escape thesis writing
so I installed singularity-3.5.3.tar.gz
and I got the same issue like you.
I replaced the "old sourmash 3.4.1 docker' with a new one and this worked
waiting now for Vibrant
when you have more time (tomorrow or so) you could try the latest singularty environment? and run the setup command and see if it will work then..
if yes I will update the documentation 👍🏽
Command used:
I have tried more than 10 times, deleting folders, and caching dirs, and it always seems to fail, either in the Sourmash or the Vibrant download step. I have tried all the solutions proposed in the topics, but none of them are working.
The error that I get:
If I manually run the following line:
It works
so It doesn't seem to be a problem of the image pulling?