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icgc-argo / workflow-roadmap

Roadmap and management for genomic data processing
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šŸ› Running workflow of nf-core framework in RDPC-QA got error #390

Closed lindaxiang closed 11 months ago

lindaxiang commented 1 year ago

Describe the bug

The workflow in nf-core framework is running properly at local, while received exception when running in RDPC-QA.

Steps To Reproduce

Steps to reproduce the behaviour:

  1. Go to 'https://wes.rdpc-qa.cancercollaboratory.org/runs'
  2. Click on 'NEW RUN'
  3. Input the following and submit RUN: Workflow URL: https://github.com/icgc-argo-workflows/dnaalnqc Workflow Params: 
    {
"study_id":"TEST-QA",
"analysis_ids":"0187b82f-1693-470a-87b8-2f1693f70ac9,4f6d6ddf-3759-4a30-ad6d-df37591a3033",
"fasta":"/nfs-dev-1-vol-qa-1/reference/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.fa",
"fasta_fai":"/nfs-dev-1-vol-qa-1/reference/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.fa.fai",
"fasta_dict":"/nfs-dev-1-vol-qa-1/reference/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.dict",
"germline_resource":"/nfs-dev-1-vol-qa-1/reference/gatk-resources/af-only-gnomad.pass-only.biallelic.snp.hg38.vcf.gz",
"germline_resource_tbi":"/nfs-dev-1-vol-qa-1/reference/gatk-resources/af-only-gnomad.pass-only.biallelic.snp.hg38.vcf.gz.tbi",
"song_url":"https://song.rdpc-qa.cancercollaboratory.org",
"score_url":"https://score.rdpc-qa.cancercollaboratory.org"
}

    Workflow Engine Params:

    {
"launchDir": "/nfs-dev-1-vol-qa-1/wfgn-launch",
"projectDir": "/nfs-dev-1-vol-qa-1/wfgn-project",
"revision": "main",
"workDir": "/nfs-dev-1-vol-qa-1/wfgn-work"
}
  4. received the following errors: 
    {
  "message": "Exception while fetching data (/_entities) : null value in entry: multiqc_config=null",
  "path": [
    "_entities"
  ],
  "extensions": {
    "code": "DOWNSTREAM_SERVICE_ERROR",
    "serviceName": "song-search",
    "query": "query($representations:[_Any!]!){_entities(representations:$representations){...on Run{producedAnalyses{analysisId analysisType}inputAnalyses{analysisId analysisType analysisState files{name size}workflow{inputs workflowName workflowVersion}}}}}",
   "variables": {
      "representations": [
        {
          "__typename": "Run",
          "runId": "wes-59e3a240195f42e68e25bfcbede866fe",
          "parameters": {
            "analysis_ids": "0187b82f-1693-470a-87b8-2f1693f70ac9,4f6d6ddf-3759-4a30-ad6d-df37591a3033",
            "nucleotides_per_second": 200000,
            "api_token": "37a6259cc0c1dae299a7866489dff0bd",
            "plaintext_email": false,
            "monochrome_logs": false,
            "study_id": "TEST-QA",
            "verifybamid2_ud": "assets/verifybamid/1000g.phase3.100k.b38.vcf.gz.dat.UD",
            "max_cpus": 16,
            "multiqc_config": null,
            "score_container_version": "5.9.0",
            "max_multiqc_email_size": "25.MB",
            "hook_url": null,
            "max_time": "240.h",
            "target_interval": null,
            "germline_resource_tbi": "/nfs-dev-1-vol-qa-1/reference/gatk-resources/af-only-gnomad.pass-only.biallelic.snp.hg38.vcf.gz.tbi",
            "tracedir": null,
            "multiqc_logo": null,
            "validate_params": true,
            "multiqc_methods_description": null,
            "verifybamid2_mu": "assets/verifybamid/1000g.phase3.100k.b38.vcf.gz.dat.mu",
            "email_on_fail": null,
            "score_url": "https://score.rdpc-qa.cancercollaboratory.org",
            "score_container": "ghcr.io/overture-stack/score",
            "fasta_dict": "/nfs-dev-1-vol-qa-1/reference/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.dict",
            "fasta_fai": "/nfs-dev-1-vol-qa-1/reference/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.fa.fai",
            "version": false,
            "publish_dir_mode": "copy",
            "input": null,
            "score_url_download": null,
            "cleanup": false,
            "enable_conda": false,
            "verifybamid2_bed": "assets/verifybamid/1000g.phase3.100k.b38.vcf.gz.dat.bed",
            "transport_parallel": null,
            "local_mode": false,
            "aws_no_sign_request": false,
            "multiqc_title": null,
            "bait_interval": null,
            "score_url_upload": null,
            "song_url": "https://song.rdpc-qa.cancercollaboratory.org",
            "fasta": "/nfs-dev-1-vol-qa-1/reference/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.fa",
            "max_memory": "128.GB",
            "tempdir": null,
            "song_container": "ghcr.io/overture-stack/song-client",
            "email": null,
            "schema_ignore_params": "genomes",
            "transport_mem": null,
            "song_container_version": "5.0.2",
            "song_url_upload": null,
            "qc_analysis_ids": null,
            "no_intervals": false,
            "target": false,
            "outdir": null,
            "autosome_non_gap": "assets/autosomes_non_gap_regions.bed",
            "help": false,
            "show_hidden_params": false,
            "song_url_download": null,
            "skip_tools": "mosdepth,verifybamid2",
            "germline_resource": "/nfs-dev-1-vol-qa-1/reference/gatk-resources/af-only-gnomad.pass-only.biallelic.snp.hg38.vcf.gz",
            "reference_base": null
          }
        }
      ]
    },
    "classification": "DataFetchingException",
    "exception": {
      "stacktrace": [
        "GraphQLError: Exception while fetching data (/_entities) : null value in entry: multiqc_config=null",
        "    at downstreamServiceError (/appDir/node_modules/@apollo/gateway/dist/executeQueryPlan.js:268:12)",
        "    at /appDir/node_modules/@apollo/gateway/dist/executeQueryPlan.js:168:57",
        "    at Array.map (<anonymous>)",
        "    at sendOperation (/appDir/node_modules/@apollo/gateway/dist/executeQueryPlan.js:168:44)",
        "    at runMicrotasks (<anonymous>)",
        "    at processTicksAndRejections (internal/process/task_queues.js:93:5)",
        "    at async executeFetch (/appDir/node_modules/@apollo/gateway/dist/executeQueryPlan.js:130:41)",
        "    at async executeNode (/appDir/node_modules/@apollo/gateway/dist/executeQueryPlan.js:82:17)",
        "    at async executeNode (/appDir/node_modules/@apollo/gateway/dist/executeQueryPlan.js:73:27)",
        "    at async executeNode (/appDir/node_modules/@apollo/gateway/dist/executeQueryPlan.js:56:40)"
      ]
    }
  }
}

Expected behaviour

The job can be kicked off and running successfully.

bhavikbhagat93 commented 1 year ago
  1. Need to reproduce on QA
  2. propose solution
  3. fix
lindaxiang commented 1 year ago

Thanks @UmmulkiramR for investigating the issue. After further investigation, the job failed because of missing required reference files in rdpc-qa. However after staging the reference files, the job failed with the same issue This issue can be closed for now.