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error pulling singularity image #175

Open selmapichot opened 7 months ago

selmapichot commented 7 months ago

Operating System

Other Linux (please specify below)

Other Linux

rocky linux 8.9

Workflow Version

v2.0.0-g52e3698

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-human-variation --bam "/rds/project/nanopore/TB23.00177/TB23.00177_T4/SLX-24559.NoIndex.PAW12603.s_1.bam" --ref "/rds/project/selma/reference/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna" --cnv --mod --sample_name "cnv_TB23_00177_T4" --out_dir "/rds/project/nanopore_pipelined/TB23_00177_t4" -profile singularity

Workflow Execution - CLI Execution Profile

singularity

What happened?

Process ended after a Run time of 00:01:25. Error 255

Relevant log output

Changed directory to /home/sl766/ondemand/data/sys/myjobs/projects/default/28.

JobID: 51328356
======
Time: Tue Apr 23 03:46:03 BST 2024
Running on master node: cpu-q-376
Current directory: /home/sl766/ondemand/data/sys/myjobs/projects/default/28

Nodes allocated:
================
cpu-q-376 cpu-q-377 cpu-q-378 cpu-q-379

Executing command:
==================
/rds/project/rds-ln0wZw3ZB98/selma/scripts/nextflow_human_variation_cnv_TB23_00177.sh 

N E X T F L O W  ~  version 23.10.1
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [b82338d3d6]
Launching `https://github.com/epi2me-labs/wf-human-variation` [serene_watson] DSL2 - revision: 52e3698431 [master]

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-human-variation v2.0.0-g52e3698
--------------------------------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : serene_watson
  containerEngine: singularity
  container      : [withLabel:wf_human_snp:ontresearch/wf-human-variation-snp:shaca21b1351b9465f98ecdb10e01bd48dbf05e0e63, withLabel:wf_human_sv:ontresearch/wf-human-variation-sv:sha69e7a43c6f21c0ea2083e9719257fb44bc35c2ba, withLabel:wf_human_mod:ontresearch/modkit:shaeedb131a939d3eea2f9bd4dbecec805c0fa20bdb, withLabel:wf_cnv:ontresearch/wf-cnv:sha428cb19e51370020ccf29ec2af4eead44c6a17c2, withLabel:wf_human_str:ontresearch/wf-human-variation-str:shaa2f49ce57886426516eadd4048b6fdf9c22c7437, withLabel:snpeff_annotation:ontresearch/snpeff:sha1acac7c26e15955ec29021b28e6ee5a5140c245e, withLabel:wf_common:ontresearch/wf-common:sha1c5febff9f75143710826498b093d9769a5edbb9, withLabel:spectre:ontresearch/spectre:sha659145073b9a1506153d3cb154d9973eabd785e3, default:ontresearch/wf-human-variation:shad3aed855cd007c653b8fc8cb16fe46c90199990f]
  launchDir      : /rds/project/rds-ln0wZw3ZB98/selma
  workDir        : /rds/project/rds-ln0wZw3ZB98/selma/work
  projectDir     : /home/sl766/.nextflow/assets/epi2me-labs/wf-human-variation
  userName       : sl766
  profile        : singularity
  configFiles    : /home/sl766/.nextflow/assets/epi2me-labs/wf-human-variation/nextflow.config

Workflow Options
  cnv            : true
  mod            : true

Main options
  sample_name    : cnv_TB23_00177_T4
  bam            : /rds/project/rds-ln0wZw3ZB98/nanopore/TB23.00177/TB23.00177_T4/SLX-24559.NoIndex.PAW12603.s_1.bam
  ref            : /rds/project/rds-ln0wZw3ZB98/selma/reference/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
  out_dir        : /rds/project/rds-ln0wZw3ZB98/nanopore_pipelined/TB23_00177_t4

!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-human-variation for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

--------------------------------------------------------------------------------
This is epi2me-labs/wf-human-variation v2.0.0-g52e3698.
--------------------------------------------------------------------------------
[-        ] process > bam_ingress:samtools_index     -
[-        ] process > bam_ingress:check_for_align... -
[-        ] process > bam_ingress:cram_to_bam        -
[-        ] process > bam_ingress:minimap2_alignment -
[-        ] process > getGenome                      -
[-        ] process > cram_cache                     -
[-        ] process > getAllChromosomesBed           -
[-        ] process > mosdepth_input                 -
[-        ] process > getVersions                    -
[-        ] process > getParams                      -
[-        ] process > get_coverage                   -
[-        ] process > readStats                      -

[-        ] process > bam_ingress:samtools_index     -
[-        ] process > bam_ingress:check_for_align... -
[-        ] process > bam_ingress:cram_to_bam        -
[-        ] process > bam_ingress:minimap2_alignment -
[-        ] process > getGenome                      -
[-        ] process > cram_cache                     -
[-        ] process > getAllChromosomesBed           -
[-        ] process > mosdepth_input                 -
[-        ] process > getVersions                    -
[-        ] process > getParams                      -
[-        ] process > get_coverage                   -
[-        ] process > readStats                      -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[-        ] process > lookup_clair3_model            -
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > concat_snp_vcfs                -
[-        ] process > sift_clinvar_snp_vcf           -
[-        ] process > vcfStats                       -
[-        ] process > report_snp:getVersions         -
[-        ] process > report_snp:getParams           -
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[-        ] process > validate_modbam                -
[-        ] process > mod:modkit                     -
[-        ] process > cnv_spectre:mosdepth           -
[-        ] process > cnv_spectre:callCNV            -
[-        ] process > cnv_spectre:bgzip_and_index... -
[-        ] process > cnv_spectre:annotate_vcf       -
[-        ] process > cnv_spectre:getVersions        -
[-        ] process > cnv_spectre:add_snp_tools_t... -
[-        ] process > cnv_spectre:getParams          -
[-        ] process > cnv_spectre:makeReport         -
[-        ] process > output_cnv                     -
[-        ] process > configure_jbrowse              -
[-        ] process > publish_artifact               -
Pulling Singularity image docker://ontresearch/wf-human-variation:shad3aed855cd007c653b8fc8cb16fe46c90199990f [cache /rds/project/rds-ln0wZw3ZB98/selma/work/singularity/ontresearch-wf-human-variation-shad3aed855cd007c653b8fc8cb16fe46c90199990f.img]
Pulling Singularity image docker://ontresearch/spectre:sha659145073b9a1506153d3cb154d9973eabd785e3 [cache /rds/project/rds-ln0wZw3ZB98/selma/work/singularity/ontresearch-spectre-sha659145073b9a1506153d3cb154d9973eabd785e3.img]
Pulling Singularity image docker://ontresearch/wf-common:sha1c5febff9f75143710826498b093d9769a5edbb9 [cache /rds/project/rds-ln0wZw3ZB98/selma/work/singularity/ontresearch-wf-common-sha1c5febff9f75143710826498b093d9769a5edbb9.img]
Pulling Singularity image docker://ontresearch/wf-human-variation-snp:shaca21b1351b9465f98ecdb10e01bd48dbf05e0e63 [cache /rds/project/rds-ln0wZw3ZB98/selma/work/singularity/ontresearch-wf-human-variation-snp-shaca21b1351b9465f98ecdb10e01bd48dbf05e0e63.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /rds/project/rds-ln0wZw3ZB98/selma/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location

[-        ] process > bam_ingress:samtools_index     -
[-        ] process > bam_ingress:check_for_align... -
[-        ] process > bam_ingress:cram_to_bam        -
[-        ] process > bam_ingress:minimap2_alignment -
[-        ] process > getGenome                      -
[-        ] process > cram_cache                     -
[-        ] process > getAllChromosomesBed           -
[-        ] process > mosdepth_input                 -
[-        ] process > getVersions                    -
[-        ] process > getParams                      -
[-        ] process > get_coverage                   -
[-        ] process > readStats                      -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[-        ] process > lookup_clair3_model            -
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > concat_snp_vcfs                -
[-        ] process > sift_clinvar_snp_vcf           -
[-        ] process > vcfStats                       -
[-        ] process > report_snp:getVersions         -
[-        ] process > report_snp:getParams           -
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[-        ] process > validate_modbam                -
[-        ] process > mod:modkit                     -
[-        ] process > cnv_spectre:mosdepth           -
[-        ] process > cnv_spectre:callCNV            -
[-        ] process > cnv_spectre:bgzip_and_index... -
[-        ] process > cnv_spectre:annotate_vcf       -
[-        ] process > cnv_spectre:getVersions        -
[-        ] process > cnv_spectre:add_snp_tools_t... -
[-        ] process > cnv_spectre:getParams          -
[-        ] process > cnv_spectre:makeReport         -
[-        ] process > output_cnv                     -
[-        ] process > configure_jbrowse              -
[-        ] process > publish_artifact               -

ERROR ~ Error executing process > 'cnv_spectre:getParams'

Caused by:
  Failed to pull singularity image
  command: singularity pull  --name ontresearch-wf-common-sha1c5febff9f75143710826498b093d9769a5edbb9.img.pulling.1713840376147 docker://ontresearch/wf-common:sha1c5febff9f75143710826498b093d9769a5edbb9 > /dev/null
  status : 255
  message:
    INFO:    Converting OCI blobs to SIF format
    INFO:    Starting build...
    Getting image source signatures
    Copying blob sha256:f9432144bf11a2ae3ffb7360b4e32f7b18c75c7c8c125274ec3cf49d0de28e24
    Copying blob sha256:0456c71d8011447360dd461b49b6a1a4cb36edf8f7250817e99ceeb0d353f06b
    Copying blob sha256:edaedc954fb53f42a7754a6e2d1b57f091bc9b11063bc445c2e325ea448f8f68
    Copying blob sha256:38cad909cfed9fb07cc2c6612612435d52302b48ebcf94a2a4b77e02b8414142
    Copying blob sha256:88397e6fd840152eca6643094559385065a6ab98a1c3c7e75eb676b9d97aad97
    Copying blob sha256:e8b63ef4ca0ca489bb848ecf9f4db232528d222a2c0bb2a599b312ce6b5b551a
    Copying blob sha256:cd889bc730171a0013130be60f28f869d7e7cc4d923396628660de9b67f7eec8
    Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
    Copying blob sha256:2042b0824681af825bf6a3c7d48cf91a218427db24a26198aaa7a2e92145081d
    Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
    Copying blob sha256:f92f5cbd83cefb6376144f8bb2f9f111e329c846a899c43ab30486a3e53f6610
    Copying blob sha256:bf9e98e95ea2237e622f7a95d952881b4098cb0eaae4f35187e3e613189c073e
    Copying blob sha256:7f6b3a5e54932fce35ad5a37222b33f2eb18beefe66f72224a9b1744aec7974d
    Copying blob sha256:eef6267c5ef5e0d57273c68577799f9e4b4840c1f045a6e58017d093d2670e96
    Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
    Copying blob sha256:f825e05f4a5f8dfa202bdab31e25e3a2e6718e73cd3b31d1d7e00ba59a57743b
    Copying blob sha256:01ee1d7d8f3ea95d01efaac76fb8297589b234848fb0368e0edc31643dc96877
    Copying blob sha256:c54b0945cd3612285ac907cf5c4a3bac8c981d91429c4b1b147c01a0db6c56ce
    Copying blob sha256:e87a621e08fb9327433e27e00de36c001682837880e399ecd473c6b6dc19dbee
    Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
    Copying config sha256:a608715a6f6a79afd5d354d18566db1676dee9f726fe9a17b26c839a03eb653a
    Writing manifest to image destination
    FATAL:   While making image from oci registry: error fetching image to cache: while building SIF from layers: conveyor failed to get: while getting config: no descriptor found for reference "49d78389c87fce0b28f147f1283e3296dffe017b0ac640a925feaf294449ce30"

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

[-        ] process > bam_ingress:samtools_index     -
[-        ] process > bam_ingress:check_for_align... -
[-        ] process > bam_ingress:cram_to_bam        -
[-        ] process > bam_ingress:minimap2_alignment -
[-        ] process > getGenome                      -
[-        ] process > cram_cache                     -
[-        ] process > getAllChromosomesBed           -
[-        ] process > mosdepth_input                 -
[-        ] process > getVersions                    -
[-        ] process > getParams                      -
[-        ] process > get_coverage                   -
[-        ] process > readStats                      -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[-        ] process > lookup_clair3_model            -
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > concat_snp_vcfs                -
[-        ] process > sift_clinvar_snp_vcf           -
[-        ] process > vcfStats                       -
[-        ] process > report_snp:getVersions         -
[-        ] process > report_snp:getParams           -
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[-        ] process > validate_modbam                -
[-        ] process > mod:modkit                     -
[-        ] process > cnv_spectre:mosdepth           -
[-        ] process > cnv_spectre:callCNV            -
[-        ] process > cnv_spectre:bgzip_and_index... -
[-        ] process > cnv_spectre:annotate_vcf       -
[-        ] process > cnv_spectre:getVersions        -
[-        ] process > cnv_spectre:add_snp_tools_t... -
[-        ] process > cnv_spectre:getParams          -
[-        ] process > cnv_spectre:makeReport         -
[-        ] process > output_cnv                     -
[-        ] process > configure_jbrowse              -
[-        ] process > publish_artifact               -
ERROR ~ Error executing process > 'cnv_spectre:getParams'

Caused by:
  Failed to pull singularity image
  command: singularity pull  --name ontresearch-wf-common-sha1c5febff9f75143710826498b093d9769a5edbb9.img.pulling.1713840376147 docker://ontresearch/wf-common:sha1c5febff9f75143710826498b093d9769a5edbb9 > /dev/null
  status : 255
  message:
    INFO:    Converting OCI blobs to SIF format
    INFO:    Starting build...
    Getting image source signatures
    Copying blob sha256:f9432144bf11a2ae3ffb7360b4e32f7b18c75c7c8c125274ec3cf49d0de28e24
    Copying blob sha256:0456c71d8011447360dd461b49b6a1a4cb36edf8f7250817e99ceeb0d353f06b
    Copying blob sha256:edaedc954fb53f42a7754a6e2d1b57f091bc9b11063bc445c2e325ea448f8f68
    Copying blob sha256:38cad909cfed9fb07cc2c6612612435d52302b48ebcf94a2a4b77e02b8414142
    Copying blob sha256:88397e6fd840152eca6643094559385065a6ab98a1c3c7e75eb676b9d97aad97
    Copying blob sha256:e8b63ef4ca0ca489bb848ecf9f4db232528d222a2c0bb2a599b312ce6b5b551a
    Copying blob sha256:cd889bc730171a0013130be60f28f869d7e7cc4d923396628660de9b67f7eec8
    Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
    Copying blob sha256:2042b0824681af825bf6a3c7d48cf91a218427db24a26198aaa7a2e92145081d
    Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
    Copying blob sha256:f92f5cbd83cefb6376144f8bb2f9f111e329c846a899c43ab30486a3e53f6610
    Copying blob sha256:bf9e98e95ea2237e622f7a95d952881b4098cb0eaae4f35187e3e613189c073e
    Copying blob sha256:7f6b3a5e54932fce35ad5a37222b33f2eb18beefe66f72224a9b1744aec7974d
    Copying blob sha256:eef6267c5ef5e0d57273c68577799f9e4b4840c1f045a6e58017d093d2670e96
    Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
    Copying blob sha256:f825e05f4a5f8dfa202bdab31e25e3a2e6718e73cd3b31d1d7e00ba59a57743b
    Copying blob sha256:01ee1d7d8f3ea95d01efaac76fb8297589b234848fb0368e0edc31643dc96877
    Copying blob sha256:c54b0945cd3612285ac907cf5c4a3bac8c981d91429c4b1b147c01a0db6c56ce
    Copying blob sha256:e87a621e08fb9327433e27e00de36c001682837880e399ecd473c6b6dc19dbee
    Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
    Copying config sha256:a608715a6f6a79afd5d354d18566db1676dee9f726fe9a17b26c839a03eb653a
    Writing manifest to image destination
    FATAL:   While making image from oci registry: error fetching image to cache: while building SIF from layers: conveyor failed to get: while getting config: no descriptor found for reference "49d78389c87fce0b28f147f1283e3296dffe017b0ac640a925feaf294449ce30"

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

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

SamStudio8 commented 7 months ago

@selmapichot Thank you for this fuller bug report! I can now see the following:

FATAL:   While making image from oci registry: error fetching image to cache: while building SIF from layers: conveyor failed to get: while getting config: no descriptor found for reference "49d78389c87fce0b28f147f1283e3296dffe017b0ac640a925feaf294449ce30"

We have found that occasionally Nextflow workflows using Singularity are unable to pull and convert images reliably. This "no descriptor found for reference" should be intermittent and eventually go away after a couple of retries. Please advise if you find that is not the case. Note that the human variation workflow will need to download a few images to be able to run, so you may be seeing this error for different images.

selmapichot commented 7 months ago

Many thanks Sam for your reply. I will retry running the workflow.

selmapichot commented 7 months ago

Hi again, I was wondering how many times approximately should I retry the workflow before getting it to work ? I have tried it few times now on different samples, and I am still having this issue unfortunately ... Many thanks, Selma.

TearsWillFall commented 7 months ago

Had the same issue. Re-running the workflow using nf did not work for me. It seems that Nextflow is not able to pull the images but if you pull them manually it works.

I ran the pull command manually each time the workflow failed and then stored the Singularity inside $NXF_SINGULARITY_CACHEDIR dir and it eventually worked

Caused by: Failed to pull singularity image command: singularity pull --name ontresearch-wf-common-sha1c5febff9f75143710826498b093d9769a5edbb9.img.pulling.1713840376147 docker://ontresearch/wf-common:sha1c5febff9f75143710826498b093d9769a5edbb9 > /dev/null

selmapichot commented 7 months ago

Many thanks for your suggestion :) can you please share the command that you used to pull manually the singularity images ? Is it ok to use the same $NXF_SINGULARITY_CACHEDIR dir for multiple samples ?

Many thanks, S

SamStudio8 commented 7 months ago

Apologies for the delay. If you are still having trouble this may be because Nextflow may attempt to pull multiple images at once with Singularity which can occasionally lead to a race condition with simultaneous writes to the Singularity cache. You may find that running the workflow again may simply avoid the race condition and the image downloads will proceed without trouble.

As that has not been the case for you, you may wish to try:

For Singularity this can be achieved by setting the environment variable SINGULARITY_DISABLE_CACHE=True.

You can run the Singularity command indicated in the error message yourself (removing the .pulling.NNNN extension), in the directory where you keep your images (usually set with NXF_SINGULARITY_CACHEDIR). Note that if you are not already setting NXF_SINGULARITY_CACHEDIR, I would strongly advise you to do so, to avoid downloading images for each workflow.

The command is in the Caused by part of your error message, for example:

Caused by:

Failed to pull singularity image

command: singularity pull --name ontresearch-wf-common-sha1c5febff9f75143710826498b093d9769a5edbb9.img.pulling.1713840376147 docker://ontresearch/wf-common:sha1c5febff9f75143710826498b093d9769a5edbb9

/dev/null

You will want to run (note the pulling.1713840376147 removed) in your NXF_SINGULARITY_CACHEDIR:

singularity pull --name ontresearch-wf-common-sha1c5febff9f75143710826498b093d9769a5edbb9.img docker://ontresearch/wf-common:sha1c5febff9f75143710826498b093d9769a5edbb9

On Sat, 27 Apr 2024, 22:20 Selma_LP, @.***> wrote:

Many thanks for your suggestion :) can you please share the command that you used to pull manually the singularity images ? Is it ok to use the same $NXF_SINGULARITY_CACHEDIR dir for multiple samples ?

Many thanks, S

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