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Support #9685

closed

[arvbox] Docker image locator not found for arvados/jobs

Added by Bharath Manicka Vasagam over 8 years ago. Updated about 8 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Peter Amstutz
Category:
-
Target version:
-
Due date:
Story points:
-

Description

Command executed:

arvados-cwl-runner ALEA_alignreads_workflow/master-workflow.cwl --fastq H3K36me3.fastq.gz --genome1_fasta CASTEiJ.fasta --genome2_fasta C57BL6NJ.fasta --output_bam1 H3K3_CAST.bam --output_bam2 H3K3_C57.bam --saifile1_prefix H3K3_CAST.sai --saifile2_prefix H3K3_C57.sai --sam_name1 H3K3_CAST.sam --sam_name2 H3K3_C57.sam --threads 4

Error log:

2016-08-02 14:15:33 arvados.cwl-runner[22972] INFO: Uploading Docker image scidap/bwa
621M / 621M 100.0% 
Collection saved as 'Docker image scidap/bwa:latest e21aee87c920'
29rky-4zz18-ywa3kbpyftautbj
2016-08-02 14:15:42 arvados.cwl-runner[22972] INFO: Uploading Docker image scidap/samtools:v1.2
131M / 131M 100.0% 
Collection saved as 'Docker image scidap/samtools:v1.2 da3c34438704'
29rky-4zz18-vh8vm6re4z28g9m
2016-08-02 14:15:45 arvados.arv-run[22972] INFO: Upload local files: "envvar-global.yml" "bwa-samse.cwl" "samtools-view.cwl" "bwa-align.cwl" "samtools-sort.cwl" "bwa-docker.yml" "append.cwl" "samtools-docker.yml" "sam_bam_sorted.cwl" "workflow.cwl" "cut.cwl" "paste.cwl" "awk_component.cwl" "master-workflow.cwl" "workflow2.cwl" 
2016-08-02 14:15:45 arvados.arv-run[22972] INFO: Uploaded to 29rky-4zz18-nvl60ekc9bp0zlj
2016-08-02 14:15:46 arvados.arv-run[22972] INFO: Upload local files: "CASTEiJ.fasta" "H3K36me3.fastq.gz" "C57BL6NJ.fasta" 
2016-08-02 14:15:57 arvados.arv-run[22972] INFO: Uploaded to 29rky-4zz18-ctxual6s8qstyle
2016-08-02 14:15:57 arvados.cwl-runner[22972] ERROR: Caught unhandled exception, marking pipeline as failed.  Error was: <HttpError 422 when requesting https://arvados.scidap.com:8000/arvados/v1/jobs?alt=json&find_or_create=true returned "Docker image locator not found for arvados/jobs">
Workflow error, try again with --debug for more information:

Related issues 1 (0 open — 1 closed)

Related to Arvados - Idea #9677: [Docs] Install guide needs to create arvados/jobs:latest Docker image as a standard objectResolvedWard Vandewege07/29/2016Actions
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 #1

Updated by Bharath Manicka Vasagam over 8 years ago

  • Status changed from New to Closed
  • Assigned To set to Peter Amstutz
  • % Done changed from 0 to 100
arv-keepdocker --pull arvados/jobs latest

arvados has a bug/limitation that it currently doesn't load the default arvados/jobs Docker image as part of its initialization

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 #2

Updated by Peter Amstutz over 8 years ago

Reported resolved.

For the record:

arv-keepdocker --pull arvados/jobs latest
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 #3

Updated by Brett Smith over 8 years ago

  • Status changed from Closed to Feedback

It sounds like we should convert this into a story to add the requisite functionality to arvbox? Reopening this until we figure out at least some resolution to make sure this doesn't keep recurring.

Related is #9677, about documenting this dependency in the Install Guide for full installs.

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 #4

Updated by Tom Morris about 8 years ago

  • Subject changed from Docker image locator not found for arvados/jobs to [arvbox] Docker image locator not found for arvados/jobs
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 #5

Updated by Tom Morris about 8 years ago

  • Status changed from Feedback to Resolved
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