no loop devices available

[dpenas-u]

Hello,

I am reaching out to you because I am encountering an error when running the minos program using the "minos.simg" image, and I am unable to resolve it.

The command I am executing is:

nextflow run -with-singularity minos.simg  nextflow/regenotype.nf  -profile medium --ref_fasta reference.fasta --manifest manifest.tsv --make_distance_matrix 

It appears that all the steps are executed successfully until it reaches the minos part. The error displayed on the screen is as follows:

N E X T F L O W  ~  version 22.04.0
Launching `nextflow/regenotype.nf` [big_chandrasekhar] DSL2 - revision: bfe1b8e0b5
executor >  local (30)
executor >  local (30)
[1c/b2812b] process > parse_manifest                     [100%] 1 of 1 ✔
[38/ad6887] process > make_vcf_for_gramtools:vcf_merge   [100%] 1 of 1 ✔
[0c/cc6992] process > make_vcf_for_gramtools:vcf_cluster [100%] 1 of 1 ✔
[da/135eb4] process > gramtools_build                    [100%] 1 of 1 ✔
[15/3b24ae] process > minos (4)                          [100%] 19 of 19, failed: 18, retries: 12 ✔
[3a/e2191a] process > make_per_sample_vcfs_dir (1)       [100%] 2 of 2, failed: 2, retries: 2
[80/232c20] process > ivcf_merge_chunks (1)              [100%] 1 of 1 ✔
[62/f3d520] process > ivcf_final_merge                   [100%] 3 of 3, failed: 3, retries: 2 ✘
[-        ] process > distance_matrix                    -
[8b/ca4db5] NOTE: Process `make_per_sample_vcfs_dir (1)` terminated with an error exit status (255) -- Execution is retried (1)
[4b/212478] NOTE: Process `make_per_sample_vcfs_dir (1)` terminated with an error exit status (255) -- Execution is retried (2)
[2a/9eeff2] NOTE: Process `ivcf_final_merge` terminated with an error exit status (255) -- Execution is retried (1)
[f7/49c909] NOTE: Process `ivcf_final_merge` terminated with an error exit status (255) -- Execution is retried (2)
Error executing process > 'ivcf_final_merge'

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

Command executed:

  cat <<"EOF" > files.txt
  work/80/232c20b8928f00a42a91876f6825c3/merged.vcf
  EOF
      ivcfmerge files.txt Compare_prueba/merged.vcf
      touch done_file

Command exit status:
  255

Command output:
  (empty)

Command error:
  FATAL:   container creation failed: mount /proc/self/fd/3->/usr/local/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/3: failed to find loop device: could not attach image file to loop device: no loop devices available

Could you please assist me in resolving this issue? Alternatively, do you have any suggestions for possible alternatives?

I have already modified the maximum number of loops available in my computer:

$cat /etc/modules
options loop max_loop=256
8192eu

loop

Thank you in advance.

[martinghunt]

Sorry but I really don't know how to help with this - it looks like a singularity error. Could be worth filing an issue with singularity, or checking the existing ones (there's a few with this error already)?

[dpenas-u]

Thanks for getting back to me and for your suggestion. I really appreciate you taking the time to help me out. I’ll definitely look into filing an issue with Singularity or checking out the existing ones. Thanks again for your help!

[dpenas-u]

In case anyone else encounters the same issue, I was able to solve the problem by referring to this Singularity issue: https://github.com/sylabs/singularity/issues/1499.