not working with singularity

[sconlan]

I have followed the instructions in the readme for downloading the databases but now I'm trying to run camitax on real genomes and I get a lot of errors:

nextflow run CAMI-challenge/CAMITAX -profile singularity --db db --i input --x fasta
...
Error executing process > 'prodigal (Sdev_DM33A01_acrmy.spades.pilon)'

Caused by:ror:
  Process `prodigal (Sdev_DM33A01_acrmy.spades.pilon)` terminated with an error exit status (1)f doesn't exist in conta
iner
Command executed: 0: cd: /gpfs/gsfs10/users/Segrelab/conlans/sandbox/camitax/work/96/da102cca5ee73b371511f6b4e610b6: No
 such file or directory
  prodigal -a Sdev_DM33A01_acrmy.spades.pilon.genes.faa -d Sdev_DM33A01_acrmy.spades.pilon.genes.fna -i Sdev_DM33A01_acrmy.spades.pilon.fasta
  grep -c "^>" Sdev_DM33A01_acrmy.spades.pilon.genes.faa > Sdev_DM33A01_acrmy.spades.pilon.genes.cnt
  /gpfs/gsfs10/users/Segrelab/conlans/sandbox/camitax/work/96/da102cca5ee73b371511f6b4e610b6
Command exit status:
  1: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Command output:
  (empty)

Command error:
  WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  /bin/bash: line 0: cd: /gpfs/gsfs10/users/Segrelab/conlans/sandbox/camitax/work/96/da102cca5ee73b371511f6b4e610b6: No such file or directory
  /bin/bash: .command.sh: No such file or directory

Work dir:
  /gpfs/gsfs10/users/Segrelab/conlans/sandbox/camitax/work/96/da102cca5ee73b371511f6b4e610b6

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

Yesterday, I was getting errors like:

Error executing process > 'mash (Scap_DM24H05_acrog.spades.pilon)'
	FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://q
Caused by:containers/mash:2.0--gsl2.2_2: pinging container registry quay.io: Get "https://quay.io/v2/": EOF
  Failed to pull singularity image
  command: singularity pull  --name quay.io-biocontainers-mash-2.0--gsl2.2_2.img.pulling.1647808897118 docker://quay.io/biocontainers/mash:2.0--gsl2.2_2 > /dev/null
  status : 255
  message:ing pending tasks (2)
	FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://quay.io/biocontainers/mash:2.0--gsl2.2_2: pinging container registry quay.io: Get "https://quay.io/v2/": EOF

Has something changes in the containers or container host? I'm using nextflow 21.10.5

[sconlan]

I'm not conversant in nextflow/singularity, but this might be relevant: bioconda/bioconda-recipes#11583