ERROR: Unknown image format/type -> Test run does not seem to work

[pmginacio]

Describe the bug I have cloned the repo and tried to run the test case. I fails with message about unknown image format.

Additional context

pedro@host$ nextflow -v
nextflow version 21.04.3.5560

pedro@host$ singularity --version
2.4.2-dist

pedro@host$ nextflow run main.nf -profile standard,test
N E X T F L O W  ~  version 21.04.3
Launching `main.nf` [golden_elion] - revision: ab68701493
executor >  local (5)
executor >  local (5)
[f0/ff3ece] process > call_snvs1 (1)  [100%] 1 of 1, failed: 1 ✘
[10/b2f904] process > call_snvs2 (1)  [200%] 2 of 1, failed: 2 ✘
[44/9c19f1] process > call_sv_del (1) [100%] 1 of 1, failed: 1 ✘
[ca/e10e4d] process > call_sv_dup (1) [100%] 1 of 1, failed: 1 ✘
[2d/8190ba] process > get_depth (1)   [100%] 1 of 1, failed: 1 ✘
[-        ] process > format_snvs     -
[-        ] process > get_core_var    -
[-        ] process > analyse_1       -
[-        ] process > analyse_2       -
[-        ] process > analyse_3       -
[-        ] process > call_stars      -
Error executing process > 'call_sv_del (1)'

Caused by:
  Process `call_sv_del (1)` terminated with an error exit status (255)

Command executed:

  graphtyper genotype_sv hg38/chr22_hg38.fasta --sam=SIM001.bam --region=chr22:42126000-42137500 --output=SIM001_sv_del cyp_hg38/sv_test.vcf.gz

Command exit status:
  255

Command output:
  (empty)

Command error:
  ERROR  : Unknown image format/type: /home/pedro/projects/stellar-pgx/containers/stellarpgx-dev.sif
  ABORT  : Retval = 255

Work dir:
  /home/pedro/projects/stellar-pgx/work/44/9c19f177e5acfa3fcd5d65fd193b5e

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

[twesigomwedavid]

@pmginacio Thanks for your interest in using StellarPGx. I see you're using Singularity v2.4.2-dist which doesn't seem to support the .sif image partitions.

We ran our StellarPGx development tests using Singularity v 3.6.3-1.osg34.el7. Any chance you could update to Singularity v 3.1 or higher?

[pmginacio]

@twesigomwedavid thank you for your reply and for sharing StellarPGx.

I installed singulatiry from the apt repository and 2.4.2-dist is the version I got. Since it met the required version stated in the description (>2.3.x), I assumed it should work.

In the mean time, I switched to using docker and it seems to work fine.

Perhaps it would make sense to up the required version for singularity in the README file.