I'm trying to use the fetchngs pipeline from nf-core (everything installed using pixi) and I encounter this error when running the test with the apptainer profile;

Core Nextflow options
  revision                  : 1.12.0
  runName                   : chaotic_stonebraker
  containerEngine           : apptainer
  launchDir                 : /home/linus/temp
  workDir                   : /home/linus/temp/work
  projectDir                : /home/linus/.nextflow/assets/nf-core/fetchngs
  userName                  : linus
  profile                   : apptainer,test
  configFiles               : 

Input/output options
  input                     : <https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv>
  outdir                    : .

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6.GB
  max_time                  : 6.h

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/fetchngs for your analysis please cite:

* The pipeline
  <https://doi.org/10.5281/zenodo.5070524>

* The nf-core framework
  <https://doi.org/10.1038/s41587-020-0439-x>

* Software dependencies
  <https://github.com/nf-core/fetchngs/blob/master/CITATIONS.md>
------------------------------------------------------
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO                                                       -
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO                                                       [  0%] 0 of 10
executor >  local (16)
executor >  local (27)
[17/b14fce] process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR9984183)                                          [  0%] 0 of 10, retries: 20
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP                                                       -
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP                                                            -
[-        ] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS -
[-        ] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH           -
[-        ] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP        -
[-        ] process > NFCORE_FETCHNGS:SRA:ASPERA_CLI                                                               -
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET                                                       -
[-        ] process > NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG                                                  -
Pulling Apptainer image <docker://quay.io/biocontainers/python:3.9--1> [cache /home/linus/temp/work/singularity/quay.io-biocontainers-python-3.9--1.img]
WARN: Apptainer cache directory has not been defined -- Remote image will be stored in the path: /home/linus/temp/work/singularity -- Use the environment variable NXF_APPTAINER_CACHEDIR to specify a different location
[2d/e11bff] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR026872)` terminated with an error exit status (1) -- Execution is retried (1)
[33/b5981f] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR12848126)` terminated with an error exit status (1) -- Execution is retried (1)
[26/6fe372] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR028935)` terminated with an error exit status (1) -- Execution is retried (1)
[ef/65fcdc] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (ERR1160846)` terminated with an error exit status (1) -- Execution is retried (1)
[12/c4521b] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR13191702)` terminated with an error exit status (1) -- Execution is retried (1)
[60/28a6ae] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR14593545)` terminated with an error exit status (1) -- Execution is retried (1)
[d0/ea2821] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR9984183)` terminated with an error exit status (1) -- Execution is retried (1)
[be/b2edef] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (GSE214215)` terminated with an error exit status (1) -- Execution is retried (1)
[dd/0de0a0] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (GSM4907283)` terminated with an error exit status (1) -- Execution is retried (1)
[b0/d5202a] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR14709033)` terminated with an error exit status (1) -- Execution is retried (1)
[2e/86a043] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR028935)` terminated with an error exit status (1) -- Execution is retried (2)
[9d/c0899f] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR026872)` terminated with an error exit status (1) -- Execution is retried (2)
[f7/34f5fd] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (ERR1160846)` terminated with an error exit status (1) -- Execution is retried (2)
[f0/99e6e6] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR13191702)` terminated with an error exit status (1) -- Execution is retried (2)
[f7/8ea876] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR14593545)` terminated with an error exit status (1) -- Execution is retried (2)
[a3/20871b] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR9984183)` terminated with an error exit status (1) -- Execution is retried (2)
[89/95079e] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (GSM4907283)` terminated with an error exit status (1) -- Execution is retried (2)
executor >  local (28)
[a0/4c72e0] process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (GSM4907283)                                          [  0%] 0 of 10, retries: 20
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP                                                       -
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP                                                            -
[-        ] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS -
[-        ] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH           -
[-        ] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP        -
[-        ] process > NFCORE_FETCHNGS:SRA:ASPERA_CLI                                                               -
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET                                                       -
[-        ] process > NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG                                                  -
Pulling Apptainer image <docker://quay.io/biocontainers/python:3.9--1> [cache /home/linus/temp/work/singularity/quay.io-biocontainers-python-3.9--1.img]
-[nf-core/fetchngs] Pipeline completed with errors-
WARN: Apptainer cache directory has not been defined -- Remote image will be stored in the path: /home/linus/temp/work/singularity -- Use the environment variable NXF_APPTAINER_CACHEDIR to specify a different location
[2d/e11bff] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR026872)` terminated with an error exit status (1) -- Execution is retried (1)
[33/b5981f] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR12848126)` terminated with an error exit status (1) -- Execution is retried (1)
[26/6fe372] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR028935)` terminated with an error exit status (1) -- Execution is retried (1)
[ef/65fcdc] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (ERR1160846)` terminated with an error exit status (1) -- Execution is retried (1)
[12/c4521b] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR13191702)` terminated with an error exit status (1) -- Execution is retried (1)
[60/28a6ae] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR14593545)` terminated with an error exit status (1) -- Execution is retried (1)
[d0/ea2821] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR9984183)` terminated with an error exit status (1) -- Execution is retried (1)
[be/b2edef] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (GSE214215)` terminated with an error exit status (1) -- Execution is retried (1)
[dd/0de0a0] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (GSM4907283)` terminated with an error exit status (1) -- Execution is retried (1)
[b0/d5202a] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR14709033)` terminated with an error exit status (1) -- Execution is retried (1)
[2e/86a043] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR028935)` terminated with an error exit status (1) -- Execution is retried (2)
[8a/29bb03] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR12848126)` terminated with an error exit status (1) -- Execution is retried (2)
[9d/c0899f] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR026872)` terminated with an error exit status (1) -- Execution is retried (2)
[f7/34f5fd] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (ERR1160846)` terminated with an error exit status (1) -- Execution is retried (2)
[f0/99e6e6] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR13191702)` terminated with an error exit status (1) -- Execution is retried (2)
[f7/8ea876] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR14593545)` terminated with an error exit status (1) -- Execution is retried (2)
[a3/20871b] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR9984183)` terminated with an error exit status (1) -- Execution is retried (2)
[89/95079e] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (GSM4907283)` terminated with an error exit status (1) -- Execution is retried (2)
[1b/66bf4e] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (GSE214215)` terminated with an error exit status (1) -- Execution is retried (2)
[d6/0a2dcf] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR14709033)` terminated with an error exit status (1) -- Execution is retried (2)
WARN: =============================================================================
  Please double-check the samplesheet that has been auto-created by the pipeline.

  Public databases don't reliably hold information such as strandedness
  information, controls etc

  All of the sample metadata obtained from the ENA has been appended
  as additional columns to help you manually curate the samplesheet before
  running nf-core/other pipelines.
===================================================================================
WARN: Killing running tasks (5)
ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR028935)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR028935)` terminated with an error exit status (1)


Command executed:

  echo DRR028935 > id.txt
  sra_ids_to_runinfo.py \
      id.txt \
      DRR028935.runinfo.tsv \
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    fuse2fs not found, will not be able to mount EXT3 filesystems
  ERROR  : Failed to create container process: Operation not permitted
Work dir:
  /home/linus/temp/work/4a/cee9dce3691bd7c21744913b7937de
Container:
  /home/linus/temp/work/singularity/quay.io-biocontainers-python-3.9--1.img

I've tried running this even with singularity, but it fails too. I'm not quite sure how do I go about fixing this, any pointers would be helpful.

Did you also install apptainer with pixi or is apptainer already installed on your system?

apptainer, nextflow and nf-core were installed using pixi as well

nextflow

and

nf-core

will be fine, but

apptainer

needs root permissions so that won't work. If you're on a system where you only user level privileges then, use

conda

instead of

apptainer

in

pixi

. If you have system admin rights then install a container system like

podman

,

docker

, or

apptainer

with those elevated privileges.

Alright got it. So unless I'm on a personal workstation, I'm going to be restricted to using conda for this purpose I suppose.

I think you can do apptainer without root https://apptainer.org/docs/admin/main/installation.html#install-unprivileged-from-pre-built-binaries