Failed to create user namespace

[lorenzoball]

hello everyone,

I am trying to use this tool to annotate my dekul run output.
it gives me this mistake : Failed to create user namespace. I don't know what this namespace is and how I can create it.
I created a conda envirnoment and installed singularity to run the tool. Here's my config file :
{
"input_file": "/bioinfo/users/lballest/new_annot_tool/merged-diff-counts.tsv.gz",
"sequence_col": "contig",
"id_col": "tag",
"map_to" : ["human"],
"human_fasta" : "/bioinfo/users/lballest/new_annot_tool/hg38.fa.gz",
"human_gff" : "/bioinfo/users/lballest/new_annot_tool/gencode.v37.annotation.gtf.gz",
"output_dir": "/data/kdi_prod/.kdi/project_workspace_0/1438/acl/02.00/Analyse/Newtool_annotB9vsWT",
"keep_col": ["contig","nb-merged-kmer","tag"],
"threads": 10,
"library_type": "stranded"
}

Thank you for your help!

[aLaine1]

Hello,
I couldn't reproduce your error, but from what I understand, this issue is caused by the Singularity installation itself.
I could see 2 reasons :

• You may have installed Singularity inside a conda environment (using "conda install"). Most singularity binaries rely on root privileges to work properly, so I would advise removing it from your conda environment and installing it directly ( https://docs.sylabs.io/guides/3.0/user-guide/installation.html )
• Maybe you are working on a server, or a computer without root privileges ? If so, you should carefully read this part of the documentation to properly set singularity parameters ( https://docs.sylabs.io/guides/3.8/admin-guide/installation.html#install-nonsetuid )
  I hope this will help you, let me know if you have any other question