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bichangwei / PMAT

An efficient assembly tool for plant mitochondrial genome
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apptainer issue with user namespace #18

Open Kai3005 opened 6 months ago

Kai3005 commented 6 months ago

when i use pmat to assembly a mito genome, a error occurred when it called up apptainer. the first , i used autoMito mode, subsequently the dir called subsample has generated successfully, but another dir did not, and it failed. i used conda install apptainer and the version of PMAT is v1.5.3，here's the error code: INFO: squashfuse not found, will not be able to mount SIF INFO: fuse2fs not found, will not be able to mount EXT3 filesystems INFO: gocryptfs not found, will not be able to use gocryptfs INFO: Converting SIF file to temporary sandbox... FATAL: while extracting runAssembly.sif: root filesystem extraction failed: extract command failed: INFO : A system administrator may need to enable user namespaces, install INFO : apptainer-suid, or compile with ./mconfig --with-suid ESC[91mERROR : Failed to create user namespace: user namespace disabled ESC[0m: exit status 1 im wondering if only admin account can use the pmat, or its woring with my code? hope to get some help

yunmika commented 6 months ago

Hi, the error is due to Apptainer not being a root install, you need to get an administrator to install it.

when i use pmat to assembly a mito genome, a error occurred when it called up apptainer. the first , i used autoMito mode, subsequently the dir called subsample has generated successfully, but another dir did not, and it failed. i used conda install apptainer and the version of PMAT is v1.5.3，here's the error code: INFO: squashfuse not found, will not be able to mount SIF INFO: fuse2fs not found, will not be able to mount EXT3 filesystems INFO: gocryptfs not found, will not be able to use gocryptfs INFO: Converting SIF file to temporary sandbox... FATAL: while extracting runAssembly.sif: root filesystem extraction failed: extract command failed: INFO : A system administrator may need to enable user namespaces, install INFO : apptainer-suid, or compile with ./mconfig --with-suid ESC[91mERROR : Failed to create user namespace: user namespace disabled ESC[0m: exit status 1 im wondering if only admin account can use the pmat, or its woring with my code? hope to get some help

tallnuttrbgv commented 5 months ago

I also have this error. It was installed by a sys admin. Have asked them to look into it. It would be very helpful it apptainer could be installed without root. Thanks.