While pulling image from oci registry: error fetching image to cache: unable to Download Image

[Linlin1213a]

(base) ubuntu@VM-16-6-ubuntu:~$ nextflow run pgscatalog/pgsc_calc \
    -profile singularity \
    --input samplesheet.csv --target_build GRCh37 \
    --pgs_id PGS003765 \
    --run_ancestry /home/ubuntu/pgsc_HGDP+1kGP_v1.tar.zst
N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/pgscatalog/pgsc_calc` [sleepy_meucci] DSL2 - revision: 8bdf287d55 [main]
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`


------------------------------------------------------
  pgscatalog/pgsc_calc v2.0.0-alpha.5-g8bdf287
------------------------------------------------------
Core Nextflow options
  revision          : main
  runName           : sleepy_meucci
  containerEngine   : singularity
  launchDir         : /home/ubuntu
  workDir           : /home/ubuntu/work
  projectDir        : /home/ubuntu/.nextflow/assets/pgscatalog/pgsc_calc
  userName          : ubuntu
  profile           : singularity
  configFiles       : 

Input/output options
  input             : samplesheet.csv
  pgs_id            : PGS003765
  outdir            : results

Reference options
  run_ancestry      : /home/ubuntu/pgsc_HGDP+1kGP_v1.tar.zst
  ref_samplesheet   : /home/ubuntu/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
  ld_grch37         : /home/ubuntu/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
  ld_grch38         : /home/ubuntu/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
  ancestry_checksums: /home/ubuntu/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/checksums.txt

Compatibility options
  target_build      : GRCh37

Matching options
  min_overlap       : 0

executor >  local (51)
[9b/d4f2a8] process > PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS003765, pgp_id:, trait_efo:])              [100%] 1 of 1 ✔
[d3/41bd5a] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                         [100%] 1 of 1 ✔
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                                          -
[skipped  ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (ukb chromosome 22)                     [100%] 24 of 24, stored: 24 ✔
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF                                                 -
[skipped  ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE (1)                                      [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS (ukb chromosome 14)                    [100%] 24 of 24, stored: 24 ✔
[skipped  ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FILTER_VARIANTS (ukb GRCh37)                              [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF (reference)                            [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:INTERSECT_THINNED (ukb)                                   [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:RELABEL_IDS (ukb null pvar)                               [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_TARGET (ukb)                               [100%] 1 of 1, stored: 1 ✔
[skipped  ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:PLINK2_ORIENT (ukb)                                       [100%] 1 of 1, stored: 1 ✔
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA                                               -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT                                           -
[f3/d4ca05] process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (ukb chromosome 18)                                   [100%] 24 of 24 ✔
[4d/9e5e76] process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE (ukb)                                                  [100%] 1 of 1 ✔
[da/272422] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_SCOREFILES (ukb additive scorefile)                    [100%] 1 of 1 ✔
[skipped  ] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ (ukb null afreq)                                 [100%] 1 of 1, stored: 1 ✔
[6a/583b68] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE (reference chromosome ALL effect type additive 0) [100%] 22 of 22 ✔
[fd/a3d4f9] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE (ukb)                                          [100%] 1 of 1 ✔
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:ANCESTRY_ANALYSIS                                                   -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT                                                        -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS                                                       -
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:ANCESTRY_PROJECT:FRAPOSA_PCA (1)'

Caused by:
  Failed to pull singularity image
  command: singularity pull  --name ghcr.io-pgscatalog-fraposa_pgsc-v0.1.0-singularity.img.pulling.1712758517206 oras://ghcr.io/pgscatalog/fraposa_pgsc:v0.1.0-singularity > /dev/null
  status : 255
  message:
    INFO:    Downloading oras image
    FATAL:   While pulling image from oci registry: error fetching image to cache: unable to Download Image: error writing layer: stream error: stream ID 1; PROTOCOL_ERROR; received from peer

 -- Check '.nextflow.log' file for details
ERROR ~ ERROR: Projection subworkflow failed

 -- Check '.nextflow.log' file for details

ERROR ~ ERROR: No results report written!

 -- Check '.nextflow.log' file for details

I noticed an error, described as follows: FATAL: While pulling image from oci registry: error fetching image to cache: unable to Download Image: error writing layer: stream error: stream ID 1; PROTOCOL_ERROR; received from peer. It seems that I failed to pull the image. Referring to the previous issues, I used the following code.

(base) ubuntu@VM-16-6-ubuntu:~$ singularity shell oras://ghcr.io/pgscatalog/fraposa_pgsc:v0.1.0-singularity
INFO:    Downloading oras image
4.1MiB / 149.5MiB [===>------------------------------------------------------------------------------------------------------------------------------------------------------------] 3 % 2.4 KiB/s 17h13m26s
FATAL:   Unable to handle oras://ghcr.io/pgscatalog/fraposa_pgsc:v0.1.0-singularity uri: unable to Download Image: error writing layer: stream error: stream ID 1; PROTOCOL_ERROR; received from peer

It seems that file download is the main reason for this failure, is there any good way to solve this problem？

[nebfield]

It looks like you have some network problems connecting to the GitHub container registry. Nextflow automatically downloads all of the required software from the container registry.

I'd suggest trying to run the workflow again with -resume because you were able to download containers for the other processes OK. There might have been a temporary problem.

If the problem persists perhaps you could ask for help from your network administrator. They might be blocking or restricting access.

[Linlin1213a]

Thanks for your quick reply. I think I have to contact the network administrator to help me deal with the network problem.