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KosinskiLab / AlphaPulldown

https://doi.org/10.1093/bioinformatics/btac749
GNU General Public License v3.0
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Error with singularity during installation #439

Open ebettler opened 1 week ago

ebettler commented 1 week ago

Hi, I followed the installation process and the command ‘singularity build --sandbox lol fold_analysis_latest.sif’ returned : INFO: Starting build... INFO: Checking the boot image fold_analysis_latest.sif WARNING: integrity: signature not found for object group 1 WARNING: The boot image could not be verified, but the build will continue. ERROR: unpackSIF failed: root filesystem extraction failed: could not extract squashfs data, unsquashfs not found FATAL: While performing build: packer failed to pack: root filesystem extraction failed: could not extract squashfs data, unsquashfs not found

Do you have a suggestion for solving the problem?

BR,

DimaMolod commented 4 days ago

Hi @ebettler, The error message you're encountering indicates that the unsquashfs utility is missing from your system. unsquashfs is part of the squashfs-tools package and is required by Singularity to extract the root filesystem from the SIF (Singularity Image Format) file during the build process. Please try to install this package e.g. for ubuntu sudo apt-get install squashfs-tools

ebettler commented 3 days ago

Thanks you for your reply. I thought so too but unsquashfs utility are already installed (computer and conda env). I've installed singularity via conda...could it be the problem source ?

ebettler commented 3 days ago

$ unsquashfs fold_analysis_latest.sif FATAL ERROR: Can't find a valid SQUASHFS superblock on fold_analysis_latest.sif

DimaMolod commented 3 days ago

The issue you're encountering is likely due to the way Singularity interacts with system utilities when installed via Conda. Although you have unsquashfs installed, Singularity installed through Conda might not be able to access system-wide utilities like unsquashfs due to environment isolation. I would recommend to install Singularity system-wide rather than within a Conda environment. Additionally, the error message from running unsquashfs fold_analysis_latest.sif suggests that the SIF file might not be a valid SquashFS filesystem or could be corrupted.You can verify your sif file with the following command singularity verify fold_analysis_latest.sif

ebettler commented 2 days ago

I've removed singularity-container from conda env. I've installed singularity package for my ubuntu 22.04 and launch the command: singularity pull docker://kosinskilab/fold_analysis:latest When i check the container with singularity verify fold_analysis_latest.sif , i've got: FATAL: Failed to verify container: integrity: signature not found for object group 1