Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.

"Workflow input processing failed" WDL v1 - Comments in input JSON

bshifawbshifaw Member, Broadie, Moderator admin

I'm getting a few warnings regarding the use of comments in my input.json but no detailed message about why the workflow is failing. I've used comments before in a json but this my first time running with wdl v1, is the use of comments in the json still valid?

[2019-01-10 22:54:04,05] [info] MaterializeWorkflowDescriptorActor [a279d538]: Parsing workflow as WDL 1.0
[2019-01-10 22:54:09,30] [error] WorkflowManagerActor Workflow a279d538-35e2-424c-b206-9ef2c6cc440d failed (during MaterializingWorkflowDescriptorState): cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anon$1: Workflow input processing fai
led:
WARNING: Unexpected input provided: #ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.BaseRecalibrator.gatk_docker
WARNING: Unexpected input provided: #ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.ApplyBQSR.gatk_docker
WARNING: Unexpected input provided: #ExomeGermlineSingleSample.haplotype_database_file
WARNING: Unexpected input provided: ##_COMMENT3
WARNING: Unexpected input provided: #ExomeGermlineSingleSample.BamToGvcf.BamToGvcf.HaplotypeCaller.gatk_docker
WARNING: Unexpected input provided: #ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.GatherBqsrReports.gatk_docker
WARNING: Unexpected input provided: #ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics
WARNING: Unexpected input provided: ##ExomeGermlineSingleSample.bait_set_name
WARNING: Unexpected input provided: ##_COMMENT2
WARNING: Unexpected input provided: #ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.SplitRG.reads_per_file
WARNING: Unexpected input provided: ##_COMMENT5
WARNING: Unexpected input provided: ##_COMMENT4
WARNING: Unexpected input provided: #ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics
WARNING: Unexpected input provided: ##_COMMENT1
WARNING: Unexpected input provided: #ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.MarkDuplicates.read_name_regex
WARNING: Unexpected input provided: #ExomeGermlineSingleSample.BamToGvcf.BamToGvcf.ValidateGVCF.gatk_docker
        at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.cromwell$engine$workflow$lifecycle$materialization$MaterializeWorkflowDescriptorActor$$workflowInitializationFailed(MaterializeWorkflowDescriptorActor.scala:214)
        at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:184)
        at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:179)
        at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)
        at akka.actor.FSM.processEvent(FSM.scala:684)
        at akka.actor.FSM.processEvent$(FSM.scala:681)
        at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.akka$actor$LoggingFSM$$super$processEvent(MaterializeWorkflowDescriptorActor.scala:135)
        at akka.actor.LoggingFSM.processEvent(FSM.scala:820)
        at akka.actor.LoggingFSM.processEvent$(FSM.scala:802)
        at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.processEvent(MaterializeWorkflowDescriptorActor.scala:135)
        at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:678)
        at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:672)
        at akka.actor.Actor.aroundReceive(Actor.scala:517)
        at akka.actor.Actor.aroundReceive$(Actor.scala:515)
        at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.aroundReceive(MaterializeWorkflowDescriptorActor.scala:135)
        at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)
        at akka.actor.ActorCell.invoke(ActorCell.scala:557)
        at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)
        at akka.dispatch.Mailbox.run(Mailbox.scala:225)
        at akka.dispatch.Mailbox.exec(Mailbox.scala:235)
        at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
        at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
        at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
        at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

Best Answers

Answers

  • bshifawbshifaw Member, Broadie, Moderator admin
    edited January 11

    This is the json

    {
    "##_COMMENT1": "SAMPLE NAME AND UNMAPPED BAMS - read the README to find other examples.",
    "ExomeGermlineSingleSample.sample_and_unmapped_bams": {
    "final_gvcf_base_name": "NA12878_20k",
    "unmapped_bam_suffix": "H06JUADXX130110.1.ATCACGAT.20k",
    "flowcell_unmapped_bams": ["gs://broad-public-datasets/NA12878_downsampled_for_testing/unmapped/H06HDADXX130110.1.ATCACGAT.20k_reads.bam",
    "gs://broad-public-datasets/NA12878_downsampled_for_testing/unmapped/H06HDADXX130110.2.ATCACGAT.20k_reads.bam",
    "gs://broad-public-datasets/NA12878_downsampled_for_testing/unmapped/H06JUADXX130110.1.ATCACGAT.20k_reads.bam"
    ],
    "sample_name": "NA12878",
    "base_file_name": "NA12878"
    },

    "##_COMMENT2": "REFERENCES",
    "ExomeGermlineSingleSample.references": {
    "break_bands_at_multiples_of": 1000000,
    "calling_interval_list": "gs://gatk-legacy-bundles/b37/wgs_calling_regions.v1.interval_list",
    "dbsnp_vcf": "gs://gatk-legacy-bundles/b37/dbsnp_138.b37.vcf.gz",
    "dbsnp_vcf_index": "gs://gatk-legacy-bundles/b37/dbsnp_138.b37.vcf.idx.gz",
    "reference_fasta": {
    "ref_fasta": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta",
    "ref_fasta_index": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta.fai",
    "ref_dict": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.dict.gz",
    "#ref_alt": "gs://gatk-legacy-bundles/b37/",
    "ref_ann": "gs://gatk-legacy-bundles/b37/v0/human_g1k_v37_decoy.fasta.ann",
    "ref_sa": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta.sa",
    "ref_amb": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta.amb",
    "ref_bwt": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta.bwt",
    "ref_pac": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta.pac"
    },
    "known_indels_sites_vcfs": [
    "gs://gatk-legacy-bundles/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz",
    "gs://gatk-legacy-bundles/b37/1000G_phase1.indels.b37.vcf.gz"
    ],
    "known_indels_sites_indices": [
    "gs://gatk-legacy-bundles/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz",
    "gs://gatk-legacy-bundles/b37/1000G_phase1.indels.b37.vcf.idx.gz"
    ],
    "contamination_sites_ud": "gs://broad-references/hg19/v0/Homo_sapiens_assembly19.contam.UD",
    "contamination_sites_bed": "gs://broad-references/hg19/v0/Homo_sapiens_assembly19.contam.bed",
    "contamination_sites_mu": "gs://broad-references/hg19/v0/Homo_sapiens_assembly19.contam.mu",
    "evaluation_interval_list": "gs://broad-references/hg19/v0/wgs_evaluation_regions.v1.interval_list",
    "haplotype_scatter_count": 50,
    "#fingerprint_genotypes_file": "File? (optional)",
    "#fingerprint_genotypes_index": " File? (optional)"
    },
    "#ExomeGermlineSingleSample.haplotype_database_file": "File? (optional)",
    "ExomeGermlineSingleSample.target_interval_list": "gs://gatk-legacy-bundles/b37/Broad.human.exome.b37.interval_list.gz",
    "##ExomeGermlineSingleSample.bait_set_name": "File",
    "ExomeGermlineSingleSample.bait_interval_list": "gs://gatk-legacy-bundles/b37/Broad.human.exome.b37.interval_list.gz",

    "##_COMMENT3": "Workflow Options",
    "#ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": "Boolean (optional, default = true)",
    "#ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.MarkDuplicates.read_name_regex": "String? (optional)",
    "#ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": "Boolean (optional, default = true)",
    "#ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.SplitRG.reads_per_file": "Int (optional, default = 48000000)",

    "##_COMMENT4": "Runtime Attributes",
    "ExomeGermlineSingleSample.papi_settings": {
    "preemptible_tries": 3,
    "agg_preemptible_tries": 3
    },

    "##_COMMENT5": "Docker",
    "#ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.ApplyBQSR.gatk_docker": "String (optional, default = \"us.gcr.io/broad-gatk/gatk:4.0.10.1\")",
    "#ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.BaseRecalibrator.gatk_docker": "String (optional, default = \"us.gcr.io/broad-gatk/gatk:4.0.10.1\")",
    "#ExomeGermlineSingleSample.BamToGvcf.BamToGvcf.HaplotypeCaller.gatk_docker": "String (optional, default = \"us.gcr.io/broad-gatk/gatk:4.0.10.1\")",
    "#ExomeGermlineSingleSample.BamToGvcf.BamToGvcf.ValidateGVCF.gatk_docker": "String (optional, default = \"us.gcr.io/broad-gatk/gatk:4.0.10.1\")",
    "#ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.GatherBqsrReports.gatk_docker": "String (optional, default = \"us.gcr.io/broad-gatk/gatk:4.0.10.1\")"

    }

  • bshifawbshifaw Member, Broadie, Moderator admin
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