singularity exec SAW_7.0.sif failed

[tenlives]

'INFO: Converting SIF file to temporary sandbox... FATAL: while extracting SAW_7.0.sif: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled : exit status 1'

When I run 'singularity exec SAW_7.0.sif mapping --runMode genomeGenerate' command, it raises this error. How to solve it for a non-root user, thank you!

[Clouate]

Hi, for non-root user, we recommend solution as follow, export SINGULARITY_CACHEDIR=/path/to/build singularity build SAW_version.sif docker:dockerhub_url

[tenlives]

Hi, for non-root user, we recommend solution as follow, export SINGULARITY_CACHEDIR=/path/to/build singularity build SAW_version.sif docker:dockerhub_url

Thank you for your reply. I followed this solution, but I still get the same error. The singularity (version 3.8.6) is installed by conda 'conda install conda-forge::singularity'.

[Clouate]

For singularity itself, you could try to contact your HPC admin to install singularity, refer the follow method when installing singularity as non-root user, or consider using docker ./mconfig --without-suid --prefix=$PATH_YOU_WANT_TO_INSTALL

Reference: https://docs.sylabs.io/guides/3.9/admin-guide/installation.html#install-from-source install-from-source->Unprivileged (non-setuid) Installation

[tenlives]

For singularity itself, you could try to contact your HPC admin to install singularity, refer the follow method when installing singularity as non-root user, or consider using docker ./mconfig --without-suid --prefix=$PATH_YOU_WANT_TO_INSTALL

Reference: https://docs.sylabs.io/guides/3.9/admin-guide/installation.html#install-from-source install-from-source->Unprivileged (non-setuid) Installation

Great, thanks! If I want to use Stereopy software to do a cell segmentaion. From SAW output, the bin1 gene expression file I have got, could you tell me how to get the ssDNA .tif image file?

[Clouate]

Hi, you could get it from 03.register, named as ${SN_number}.regist.tif. I'm not sure if there are other tif files in your directory. Please obtain the file with the suffix 'regist.tif', whose coordinates are consistent with the gene expression matrix.

[tenlives]

Hi, you could get it from 03.register, named as ${SN_number}.regist.tif. I'm not sure if there are other tif files in your directory. Please obtain the file with the suffix 'regist.tif', whose coordinates are consistent with the gene expression matrix.

Thank you! When I run SAW whole pipeline to get 03.register,I met this error https://github.com/STOmics/SAW/issues/96 . Could help me to fix it?