Bedtool image

[aheravi]

Description of the bug

Failed to pull BEDTOOLS singularity image

Command used and terminal output

Sep.-20 18:49:13.796 [Task submitter] INFO  nextflow.Session - [3b/0db9e9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATE
S_PICARD:SAMTOOLS_INDEX (F147162)
Sep.-20 18:49:13.806 [Actor Thread 126] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (1); work-dir=null
  error [java.lang.IllegalStateException]: java.lang.IllegalStateException: Failed to pull singularity image
  command: singularity pull  --name community.wave.seqera.io-library-bedtools_coreutils-ba273c06a3909a15.img.pulling.1726883351688 or
as://community.wave.seqera.io/library/bedtools_coreutils:ba273c06a3909a15 > /dev/null
  status : 255
  message:
    [31mFATAL:  ESC[0m While pulling image from oci registry: failed to get checksum for //community.wave.seqera.io/library/bedtools_
coreutils:ba273c06a3909a15: no layer found corresponding to SIF image

Relevant files

No response

System information

No response

[aheravi]

It sounds like the error was singularity version issue.

[tud03125]

I also come across that problem too. In addition, when tried "singularity pull" on the specific "bedtools," it didn't resolve it.

[aheravi]

Mine resolved using apptainer.

[tud03125]

I wish I could use apptainer. My Tempe HPC system don't have apptainer (in addition to docker!) and won't install them for a while.