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ERROR ~ Error executing process > 'wf_dorado:dorado (10)' Caused by: Failed to pull singularity image #55

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Ashok-pappu opened this issue Nov 18, 2024 · 2 comments
Open

ERROR ~ Error executing process > 'wf_dorado:dorado (10)' Caused by: Failed to pull singularity image #55

Ashok-pappu opened this issue Nov 18, 2024 · 2 comments

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@Ashok-pappu
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Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

wf-basecalling v1.4.2-g9c0f9db

Workflow Execution

Command line (Local)

Other workflow execution

No response

EPI2ME Version

v1.4.2

CLI command run

#nextflow run epi2me-labs/wf-basecalling \

--basecaller_cfg '[email protected]' \

--dorado_ext 'pod5' \

--input /lustre/ashokkumar/nanopore/basecall/Nanopore_run01/pod5 \

--outdir /lustre/ashokkumar/nanopore/basecall/Nanopore_run01 \

--remora_cfg [email protected]_5mCG_5hmCG@v2 \

-with-singularity /lustre/ashokkumar/nanopore/wf-common.sif \

-profile singularity

nextflow run epi2me-labs/wf-basecalling
--basecaller_cfg '[email protected]'
--dorado_ext 'pod5'
--input '/lustre/ashokkumar/nanopore/basecall/Nanopore_run01/pod5'
--ref '/lustre/ashokkumar/nanopore/basecall/Nanopore_run01//test/wf-basecalling-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta'
--remora_cfg '[email protected]_5mCG_5hmCG@v2'
-profile singularity
-with-singularity /lustre/ashokkumar/nanopore/wf-common.sif

Workflow Execution - CLI Execution Profile

singularity

What happened?

While pulling .sif image from the docker.
Caused by:
ERROR ~ Error executing process > 'wf_dorado:dorado (10)'

Failed to pull singularity image
command: singularity pull --name ontresearch-dorado-sha8bc19cc3c78c1ce847fbf4a879cad997b7e8c430.img.pulling.1731924914859 docker://ontresearc>

Relevant log output

N E X T F L O W   ~  version 24.10.0

Launching `https://github.com/epi2me-labs/wf-basecalling` [grave_hodgkin] DSL2 - revision: 9c0f9dbf02 [master]

WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-basecalling v1.4.2-g9c0f9db
--------------------------------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : grave_hodgkin
containerEngine: singularity
  container      : [withLabel:wf_basecalling:ontresearch/dorado:sha8bc19cc3c78c1ce847fbf4a879cad997b7e8c430, withLabel:wf_common:ontresearch/wf-co>
  launchDir      : /lustre/ashokkumar/nanopore/basecall/Nanopore_run01/pod5
  workDir        : /lustre/ashokkumar/nanopore/basecall/Nanopore_run01/pod5/work
  projectDir     : /home/ashokkumar/.nextflow/assets/epi2me-labs/wf-basecalling
  userName       : ashokkumar
  profile        : singularity
  configFiles    : /home/ashokkumar/.nextflow/assets/epi2me-labs/wf-basecalling/nextflow.config

Input Options
  input          : /lustre/ashokkumar/nanopore/basecall/Nanopore_run01/pod5
  ref            : /lustre/ashokkumar/nanopore/basecall/Nanopore_run01//test/wf-basecalling-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta

Basecalling options
  basecaller_cfg : [email protected]
  remora_cfg     : [email protected]_5mCG_5hmCG@v2

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

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


--------------------------------------------------------------------------------
This is epi2me-labs/wf-basecalling v1.4.2-g9c0f9db.
--------------------------------------------------------------------------------
[-        ] prepare_reference:faidx -
[-        ] prepare_reference:faidx      -
[-        ] prepare_reference:cram_cache -
[-        ] prepare_reference:make_mmi   -
[-        ] wf_dorado:dorado             -
[-        ] wf_dorado:align_and_qsFilter -
[-        ] wf_dorado:merge_pass_calls   -
[-        ] wf_dorado:merge_fail_calls   -
[-        ] getVersions                  -
[-        ] getParams                    -
[-        ] bamstats                     -
[-        ] progressive_stats            -
[-        ] makeReport                   -
[-        ] output_last                  -
[-        ] output_stream                -

executor >  local (2)
[61/190806] prepare_reference:faidx (1)    | 0 of 1
[91/f4d38c] pre ^` e_reference:cram_cache (1) | 0 of 1
[-        ] prepare_reference:make_mmi     -
[-        ] wf_dorado:dorado               -
[-        ] wf_dorado:align_and_qsFilter   -
[-        ] wf_dorado:merge_pass_calls     -
[-        ] wf_dorado:merge_fail_calls     -
[-        ] getVersions                    -
[-        ] getParams                      -
[-        ] bamstats                       -
[-        ] progressive_stats              -
[-        ] makeReport                     -
[-        ] output_last                    -
[-        ] output_stream                  -
Pulling Singularity image docker://ontresearch/dorado:sha8bc19cc3c78c1ce847fbf4a879cad997b7e8c430 [cache /lustre/ashokkumar/nanopore/basecall/Nano>
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /lustre/ashokkumar/nanopore/basecall/Nanopore_r>

executor >  local (2)
[61/190806] prepare_reference:faidx (1)    | 0 of 1
[91/f4d38c] pre ^` e_reference:cram_cache (1) | 0 of 1
[-        ] prepare_reference:make_mmi     -
[-        ] wf_dorado:dorado               -
[-        ] wf_dorado:align_and_qsFilter   -
[-        ] wf_dorado:merge_pass_calls     -
[-        ] wf_dorado:merge_fail_calls     -
[-        ] getVersions                    -
[-        ] getParams                      -
[-        ] bamstats                       -
[-        ] progressive_stats              -
[-        ] makeReport                     -
[-        ] output_last                    -
[-        ] output_stream                  -
Pulling Singularity image docker://ontresearch/dorado:sha8bc19cc3c78c1ce847fbf4a879cad997b7e8c430 [cache /lustre/ashokkumar/nanopore/basecall/Nano>
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /lustre/ashokkumar/nanopore/basecall/Nanopore_r>

executor >  local (2)
[61/190806] prepare_reference:faidx (1)    | 1 of 1  ^|^t
[91/f4d38c] pre ^` e_reference:cram_cache (1) | 0 of 1
[-        ] prepare_reference:make_mmi     -
[-        ] wf_dorado:dorado               -
[-        ] wf_dorado:align_and_qsFilter   -
[-        ] wf_dorado:merge_pass_calls     -
[-        ] wf_dorado:merge_fail_calls     -
[-        ] getVersions                    -
[-        ] getParams                      -
[-        ] bamstats                       -
[-        ] progressive_stats              -
[-        ] makeReport                     -
[-        ] output_last                    -
[-        ] output_stream                  -
Pulling Singularity image docker://ontresearch/dorado:sha8bc19cc3c78c1ce847fbf4a879cad997b7e8c430 [cache /lustre/ashokkumar/nanopore/basecall/Nano>
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /lustre/ashokkumar/nanopore/basecall/Nanopore_r>

executor >  local (2)
[61/190806] prepare_reference:faidx (1)    | 1 of 1  ^|^t
[91/f4d38c] pre ^` e_reference:cram_cache (1) | 1 of 1  ^|^t
[-        ] prepare_reference:make_mmi     -
[-        ] wf_dorado:dorado               -
[-        ] wf_dorado:align_and_qsFilter   -
[-        ] wf_dorado:merge_pass_calls     -
[-        ] wf_dorado:merge_fail_calls     -
[-        ] getVersions                    -
[-        ] getParams                      -
[-        ] bamstats                       -
[-        ] progressive_stats              -
[-        ] makeReport                     -
[-        ] output_last                    -
[-        ] output_stream                  -



executor >  local (2)
[61/190806] prepare_reference:faidx (1)    | 1 of 1  ^|^t
[91/f4d38c] pre ^` e_reference:cram_cache (1) | 1 of 1  ^|^t
[-        ] prepare_reference:make_mmi     -
[-        ] wf_dorado:dorado               -
[-        ] wf_dorado:align_and_qsFilter   -
[-        ] wf_dorado:merge_pass_calls     -
[-        ] wf_dorado:merge_fail_calls     -
[-        ] getVersions                    -
[-        ] getParams                      -
[-        ] bamstats                       -
[-        ] progressive_stats              -
[-        ] makeReport                     -
[-        ] output_last                    -
[-        ] output_stream                  -
ERROR ~ Error executing process > 'wf_dorado:dorado (10)'

Caused by:
  Failed to pull singularity image
    command: singularity pull  --name ontresearch-dorado-sha8bc19cc3c78c1ce847fbf4a879cad997b7e8c430.img.pulling.1731924914859 docker://ontresearc>
    status : 143
    hint   : Try and increase singularity.pullTimeout in the config (current is "20m")
    message:
      INFO:    Converting OCI blobs to SIF format
      INFO:    Starting build...
 Getting image source signatures
      Copying blob sha256:b549f31133a955f68f9fa0d93f18436c4a180e12184b999a8ecf14f7eaa83309
      Copying blob sha256:a0bad51e1731c71de34c6158f8b37cb48db284732b30352cd2a83507ae7f3265
      Copying blob sha256:f7778ea3b9cc920f03f663871775029bce2916fa30ab7861050cb661d27b2b32
      Copying blob sha256:e02ba321f2159e64b39dae91caa5189b7d17f28160b35c559521751f5931c346
      Copying blob sha256:a9e5e49da50d475e92629db642aaf5a462a952b426f92934ca4e22ffec23d3de
      Copying blob sha256:16a53aaedebb92970d5d04f51f0111447e3a0644e17db10d549ba3715680b0ee
      Copying blob sha256:695fbd54ccca89540f1e97601adca51863612671eedf356563f04b678eec2249
      Copying blob sha256:84ba795f26c8dde201b0f9e8983e2fda2d7fe9b531bc444633e5a12541d45ce2
      Copying blob sha256:fa10ccbd03d9a5d733b5775dc38077afe686952abf34c7b2c8f384cdf2bf2dfd
      Copying blob sha256:e3bf7edf51fbf9cdfb97c6c3516ac3eb1fba7d713b5e5776a560c4eeaa57b4c1
      Copying blob sha256:d47b27377a017e4fe49de515b2891ef5f40015083efa255a4f1b127cdd57c684
      Copying blob sha256:8f3081e41c01332c0d6b4c227e780bc74b452e9d85e6b59d941ac6c230cdc3af
      Copying blob sha256:29c2142e67849ce2b7a2f9caadc676961a74a1fb948a2f67f794bae46af5e70a
      Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
      Copying blob sha256:7765cf1e97758329ddc8a31b9cdc563c8d6f75221c84df479bedadc9a0b9a5b4
      Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
      Copying blob sha256:1bbc24c0831bb6f64b47ba99de20fdeb8f6b7ddb56e73ab9442f6a42f01e0eee
 Copying blob sha256:46b9213974e008e86dcac73f69d1e6f057fbeb10bf088d2395f005a45c9fb911
      Copying blob sha256:77d45aba978f19eebcfcc8fd31776ee17731b1fea5dbba693dec112b1ab1c208
      Copying blob sha256:b1906776968d1fca313bfb67630f6e3ac3d140f882b5fb438366ce605dfa2ff4
      Copying blob sha256:55d3c88f8f958143710a653f435cefc36237151b06b528701ded5f40c63ca0b0
      Copying blob sha256:0282bfd5e1752d6d3b7a2d69422a6f7a8a08ee037de36b19d71905e531d0433c
      Copying blob sha256:3916be3faa164c433240dbfae1c4062ab512dfdadb18cab5733183eb90f0efcb
      Copying blob sha256:b783c4ef990dde698cf867fac98cd272ece2efaad5295c33b075edda9ca29382
      Copying blob sha256:8f2316484a95a6c3cd6063f9c3cc9865ec79cf3577ccef4f41171a5df301d009



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

executor >  local (2)
[61/190806] prepare_reference:faidx (1)    | 1 of 1  ^|^t
[91/f4d38c] pre ^` e_reference:cram_cache (1) | 1 of 1  ^|^t
[-        ] prepare_reference:make_mmi     -
[-        ] wf_dorado:dorado               -
[-        ] wf_dorado:align_and_qsFilter   -
[-        ] wf_dorado:merge_pass_calls     -
[-        ] wf_dorado:merge_fail_calls     -
[-        ] getVersions                    -
[-        ] getParams                      -
[-        ] bamstats                       -
[-        ] progressive_stats              -
[-        ] makeReport                     -
[-        ] output_last                    -
[-        ] output_stream                  -
ERROR ~ Error executing process > 'wf_dorado:dorado (10)'

Caused by:
  Failed to pull singularity image
 command: singularity pull  --name ontresearch-dorado-sha8bc19cc3c78c1ce847fbf4a879cad997b7e8c430.img.pulling.1731924914859 docker://ontresearc>
    status : 143
    hint   : Try and increase singularity.pullTimeout in the config (current is "20m")
    message:
      INFO:    Converting OCI blobs to SIF format
      INFO:    Starting build...
      Getting image source signatures
      Copying blob sha256:b549f31133a955f68f9fa0d93f18436c4a180e12184b999a8ecf14f7eaa83309
      Copying blob sha256:a0bad51e1731c71de34c6158f8b37cb48db284732b30352cd2a83507ae7f3265
      Copying blob sha256:f7778ea3b9cc920f03f663871775029bce2916fa30ab7861050cb661d27b2b32
      Copying blob sha256:e02ba321f2159e64b39dae91caa5189b7d17f28160b35c559521751f5931c346
      Copying blob sha256:a9e5e49da50d475e92629db642aaf5a462a952b426f92934ca4e22ffec23d3de
      Copying blob sha256:16a53aaedebb92970d5d04f51f0111447e3a0644e17db10d549ba3715680b0ee
      Copying blob sha256:695fbd54ccca89540f1e97601adca51863612671eedf356563f04b678eec2249
      Copying blob sha256:84ba795f26c8dde201b0f9e8983e2fda2d7fe9b531bc444633e5a12541d45ce2
      Copying blob sha256:fa10ccbd03d9a5d733b5775dc38077afe686952abf34c7b2c8f384cdf2bf2dfd
      Copying blob sha256:e3bf7edf51fbf9cdfb97c6c3516ac3eb1fba7d713b5e5776a560c4eeaa57b4c1
      Copying blob sha256:d47b27377a017e4fe49de515b2891ef5f40015083efa255a4f1b127cdd57c684
      Copying blob sha256:8f3081e41c01332c0d6b4c227e780bc74b452e9d85e6b59d941ac6c230cdc3af
      Copying blob sha256:29c2142e67849ce2b7a2f9caadc676961a74a1fb948a2f67f794bae46af5e70a
      Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
      Copying blob sha256:7765cf1e97758329ddc8a31b9cdc563c8d6f75221c84df479bedadc9a0b9a5b4
      Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
      Copying blob sha256:1bbc24c0831bb6f64b47ba99de20fdeb8f6b7ddb56e73ab9442f6a42f01e0eee
      Copying blob sha256:46b9213974e008e86dcac73f69d1e6f057fbeb10bf088d2395f005a45c9fb911
 Copying blob sha256:77d45aba978f19eebcfcc8fd31776ee17731b1fea5dbba693dec112b1ab1c208
      Copying blob sha256:b1906776968d1fca313bfb67630f6e3ac3d140f882b5fb438366ce605dfa2ff4
      Copying blob sha256:55d3c88f8f958143710a653f435cefc36237151b06b528701ded5f40c63ca0b0
      Copying blob sha256:0282bfd5e1752d6d3b7a2d69422a6f7a8a08ee037de36b19d71905e531d0433c
      Copying blob sha256:3916be3faa164c433240dbfae1c4062ab512dfdadb18cab5733183eb90f0efcb
      Copying blob sha256:b783c4ef990dde698cf867fac98cd272ece2efaad5295c33b075edda9ca29382
      Copying blob sha256:8f2316484a95a6c3cd6063f9c3cc9865ec79cf3577ccef4f41171a5df301d009



 -- 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
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This looks like an issue with Singularity timing out - I suggest speaking to your system administrator about this in the first instance.

@Ashok-pappu
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Thank you!

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@SamStudio8 @Ashok-pappu