search

cgroza / GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
Other
121 stars 6 forks source link

FATAL: Extraction failed (cache disk quote issue) #37

Closed TobyBaril closed 3 months ago

TobyBaril commented 3 months ago

Hi!

I'm pretty new to singularity and apptainer so maybe this is something quite simple. I'm getting the following error for my run:

FATAL:   while extracting /data/toby/troutGenomics/graffite_parameters/work/singularity/cgroza-collection-graffite-latest.img: root filesystem extraction failed: failed to copy content in staging file: write /tmp/rootfs-1132018289/archive-4076445747: disk quota exceeded

I think this is to do with the cache directory. I've tried to set this by setting the variables: NXF_APPTAINER_CACHEDIR=/data/toby/tmp/ and SINGULARITY_CACHEDIR=/data/toby/tmp/ but I'm still getting the same error. Is there a way to change the cache directory so I can get this to run?

Thanks!

clemgoub commented 3 months ago

Hi Toby!

Do you get this after running the command directly on a compute node? Maybe try to follow these instructions ("If using from a local apptainer image and with a clone of the Github repository:") to directly download the image while on a login node, and then run GraffiTE on a compute node with the flag -with-singularity <imagePath>.

Did you also try modifying Nextflow's config file? This is usually how I solve my tmpdir issues!

Let us know, and maybe @cgroza will be also able to chime in!

Cheers,

Clément

TobyBaril commented 3 months ago

Thanks Clément!

I should've read more into the docs! I've altered the /tmp binding - but in my case squashfuse was actually missing and needed to be installed (weird...always thought it came with singularity!). Most likely just a weird thing on our server here!

Cheers!