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Error running gatk4-genome-processing-pipeline workflow

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    Genevieve Brandt

    Hi Maria Akimenkova, could you share what is in this file?

    /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/e4e542e3-3aa2-48ab-9966-68eac94f9e9a/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/3500db78-3b4d-470a-8f8b-f896958603d4/call-GetBwaVersion/execution/stderr

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    Maria Akimenkova

    Thank you very much for answering! There is no file "stderr", only "stderr.background": https://drive.google.com/file/d/1DTFG62k3oF3Vc8QnFv-C--AqI0b04Yif/view?usp=sharing

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    Beri Shifaw

    Hi Maria Akimenkova,

    Have you installed docker on the system running the workflow? The stderr file error message:

    "docker: command not found" 

    indicates cromwell is having trouble running docker. 

    The following doc might be useful:
    How-to-Run-GATK-in-a-Docker-container - Specifically "1. Install Docker"

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    Maria Akimenkova

    Thank you very much! 
    I followed this https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4 and there was no mention of Docker. I followed your instructions and now there is another error that I don't understand.

     

    [2020-10-19 16:47:08,38] [info] Running with database db.url = jdbc:hsqldb:mem:6aae4384-7922-4ba8-8514-41e2cfc57b6d;shutdown=false;hsqldb.tx=mvcc
    [2020-10-19 16:47:13,21] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
    [2020-10-19 16:47:13,22] [info] [RenameWorkflowOptionsInMetadata] 100%
    [2020-10-19 16:47:13,27] [info] Running with database db.url = jdbc:hsqldb:mem:c9c0bc5c-3a6a-41a4-b0f0-c8127cd565a4;shutdown=false;hsqldb.tx=mvcc
    [2020-10-19 16:47:13,50] [info] Slf4jLogger started
    [2020-10-19 16:47:13,63] [info] Workflow heartbeat configuration:
    {
    "cromwellId" : "cromid-8a2ac52",
    "heartbeatInterval" : "2 minutes",
    "ttl" : "10 minutes",
    "failureShutdownDuration" : "5 minutes",
    "writeBatchSize" : 10000,
    "writeThreshold" : 10000
    }
    [2020-10-19 16:47:13,66] [info] Metadata summary refreshing every 1 second.
    [2020-10-19 16:47:13,67] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
    [2020-10-19 16:47:13,67] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
    [2020-10-19 16:47:13,68] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
    [2020-10-19 16:47:13,68] [warn] 'docker.hash-lookup.gcr-api-queries-per-100-seconds' is being deprecated, use 'docker.hash-lookup.gcr.throttle' instead (see reference.conf)
    [2020-10-19 16:47:13,81] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
    [2020-10-19 16:47:13,83] [info] SingleWorkflowRunnerActor: Version 53.1
    [2020-10-19 16:47:13,84] [info] SingleWorkflowRunnerActor: Submitting workflow
    [2020-10-19 16:47:13,87] [info] Unspecified type (Unspecified version) workflow 439d021c-71be-4340-a130-c2f750b174b1 submitted
    [2020-10-19 16:47:13,88] [info] SingleWorkflowRunnerActor: Workflow submitted 439d021c-71be-4340-a130-c2f750b174b1
    [2020-10-19 16:47:13,88] [info] 1 new workflows fetched by cromid-8a2ac52: 439d021c-71be-4340-a130-c2f750b174b1
    [2020-10-19 16:47:13,89] [info] WorkflowManagerActor Starting workflow 439d021c-71be-4340-a130-c2f750b174b1
    [2020-10-19 16:47:13,89] [info] WorkflowManagerActor Successfully started WorkflowActor-439d021c-71be-4340-a130-c2f750b174b1
    [2020-10-19 16:47:13,89] [info] Retrieved 1 workflows from the WorkflowStoreActor
    [2020-10-19 16:47:13,91] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
    [2020-10-19 16:47:13,95] [info] MaterializeWorkflowDescriptorActor [439d021c]: Parsing workflow as WDL 1.0
    [2020-10-19 16:47:15,24] [info] MaterializeWorkflowDescriptorActor [439d021c]: Call-to-Backend assignments: UnmappedBamToAlignedBam.MarkDuplicates -> Local, VariantCalling.MergeVCFs -> Local, BamToCram.ConvertToCram -> Local, AggregatedBamQC.CalculateReadGroupChecksum -> Local, AggregatedBamQC.CheckFingerprint -> Local, VariantCalling.MergeBamouts -> Local, SplitLargeReadGroup.SumSplitAlignedSizes -> Local, UnmappedBamToAlignedBam.SortSampleBam -> Local, UnmappedBamToAlignedBam.GetBwaVersion -> Local, UnmappedBamToAlignedBam.CheckContamination -> Local, SplitLargeReadGroup.SamToFastqAndBwaMemAndMba -> Local, SplitLargeReadGroup.SamSplitter -> Local, WholeGenomeGermlineSingleSample.CollectRawWgsMetrics -> Local, UnmappedBamToAlignedBam.BaseRecalibrator -> Local, UnmappedBamToAlignedBam.CollectUnsortedReadgroupBamQualityMetrics -> Local, VariantCalling.HaplotypeCallerGATK4 -> Local, UnmappedBamToAlignedBam.CollectQualityYieldMetrics -> Local, VariantCalling.HaplotypeCallerGATK3 -> Local, UnmappedBamToAlignedBam.CreateSequenceGroupingTSV -> Local, AggregatedBamQC.CollectAggregationMetrics -> Local, VariantCalling.ValidateVCF -> Local, VariantCalling.SortBamout -> Local, SplitLargeReadGroup.GatherMonolithicBamFile -> Local, AggregatedBamQC.CollectReadgroupBamQualityMetrics -> Local, UnmappedBamToAlignedBam.GatherBqsrReports -> Local, BamToCram.ValidateCram -> Local, UnmappedBamToAlignedBam.SamToFastqAndBwaMemAndMba -> Local, UnmappedBamToAlignedBam.CrossCheckFingerprints -> Local, VariantCalling.CollectVariantCallingMetrics -> Local, BamToCram.CheckPreValidation -> Local, VariantCalling.ScatterIntervalList -> Local, UnmappedBamToAlignedBam.SumFloats -> Local, WholeGenomeGermlineSingleSample.CollectWgsMetrics -> Local, UnmappedBamToAlignedBam.GatherBamFiles -> Local, UnmappedBamToAlignedBam.ApplyBQSR -> Local
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [memory, disks, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [disks, memory, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [memory, disks, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [memory, disks, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, disks, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,35] [warn] Local [439d021c]: Key/s [preemptible, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,36] [warn] Local [439d021c]: Key/s [memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,36] [warn] Local [439d021c]: Key/s [preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,36] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,36] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:15,36] [warn] Local [439d021c]: Key/s [preemptible, memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
    [2020-10-19 16:47:18,83] [info] Not triggering log of token queue status. Effective log interval = None
    [2020-10-19 16:47:19,57] [info] df932bf3-282e-49dc-b3ff-f25779b589a5-SubWorkflowActor-SubWorkflow-UnmappedBamToAlignedBam:-1:1 [df932bf3]: Starting UnmappedBamToAlignedBam.GetBwaVersion
    [2020-10-19 16:47:19,94] [info] Assigned new job execution tokens to the following groups: 439d021c: 1
    [2020-10-19 16:47:20,60] [info] df932bf3-282e-49dc-b3ff-f25779b589a5-SubWorkflowActor-SubWorkflow-UnmappedBamToAlignedBam:-1:1 [df932bf3]: Starting UnmappedBamToAlignedBam.CreateSequenceGroupingTSV
    [2020-10-19 16:47:20,95] [info] Assigned new job execution tokens to the following groups: 439d021c: 1
    [2020-10-19 16:47:21,28] [warn] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.GetBwaVersion:NA:1]: Unrecognized runtime attribute keys: memory
    [2020-10-19 16:47:21,31] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.GetBwaVersion:NA:1]: # not setting set -o pipefail here because /bwa has a rc=1 and we dont want to allow rc=1 to succeed because
    # the sed may also fail with that error and that is something we actually want to fail on.
    /usr/gitc/bwa 2>&1 | \
    grep -e '^Version' | \
    sed 's/Version: //'
    [2020-10-19 16:47:21,35] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.GetBwaVersion:NA:1]: executing: # make sure there is no preexisting Docker CID file
    rm -f /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-GetBwaVersion/execution/docker_cid
    # run as in the original configuration without --rm flag (will remove later)
    docker run \
    --cidfile /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-GetBwaVersion/execution/docker_cid \
    -i \
    \
    --entrypoint /bin/bash \
    -v /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-GetBwaVersion:/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-GetBwaVersion:delegated \
    us.gcr.io/broad-gotc-prod/genomes-in-the-cloud@sha256:93ae8b895f4e83dfc20dd2651e87baccac7dd2cbe0af602bf50afcc4b9e6f925 /cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-GetBwaVersion/execution/script

    # get the return code (working even if the container was detached)
    rc=$(docker wait cat /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-GetBwaVersion/execution/docker_cid)

    # remove the container after waiting
    docker rm cat /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-GetBwaVersion/execution/docker_cid

    # return exit code
    exit $rc
    [2020-10-19 16:47:21,86] [warn] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.CreateSequenceGroupingTSV:NA:1]: Unrecognized runtime attribute keys: preemptible, memory
    [2020-10-19 16:47:21,87] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.CreateSequenceGroupingTSV:NA:1]: python <<CODE
    with open("/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CreateSequenceGroupingTSV/inputs/121941983/Homo_sapiens_assembly38.dict", "r") as ref_dict_file:
    sequence_tuple_list = []
    longest_sequence = 0
    for line in ref_dict_file:
    if line.startswith("@SQ"):
    line_split = line.split("\t")
    # (Sequence_Name, Sequence_Length)
    sequence_tuple_list.append((line_split[1].split("SN:")[1], int(line_split[2].split("LN:")[1])))
    longest_sequence = sorted(sequence_tuple_list, key=lambda x: x[1], reverse=True)[0][1]
    # We are adding this to the intervals because hg38 has contigs named with embedded colons and a bug in GATK strips off
    # the last element after a :, so we add this as a sacrificial element.
    hg38_protection_tag = ":1+"
    # initialize the tsv string with the first sequence
    tsv_string = sequence_tuple_list[0][0] + hg38_protection_tag
    temp_size = sequence_tuple_list[0][1]
    for sequence_tuple in sequence_tuple_list[1:]:
    if temp_size + sequence_tuple[1] <= longest_sequence:
    temp_size += sequence_tuple[1]
    tsv_string += "\t" + sequence_tuple[0] + hg38_protection_tag
    else:
    tsv_string += "\n" + sequence_tuple[0] + hg38_protection_tag
    temp_size = sequence_tuple[1]
    # add the unmapped sequences as a separate line to ensure that they are recalibrated as well
    with open("sequence_grouping.txt","w") as tsv_file:
    tsv_file.write(tsv_string)
    tsv_file.close()

    tsv_string += '\n' + "unmapped"

    with open("sequence_grouping_with_unmapped.txt","w") as tsv_file_with_unmapped:
    tsv_file_with_unmapped.write(tsv_string)
    tsv_file_with_unmapped.close()
    CODE
    [2020-10-19 16:47:21,88] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.CreateSequenceGroupingTSV:NA:1]: executing: # make sure there is no preexisting Docker CID file
    rm -f /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CreateSequenceGroupingTSV/execution/docker_cid
    # run as in the original configuration without --rm flag (will remove later)
    docker run \
    --cidfile /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CreateSequenceGroupingTSV/execution/docker_cid \
    -i \
    \
    --entrypoint /bin/bash \
    -v /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CreateSequenceGroupingTSV:/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CreateSequenceGroupingTSV:delegated \
    us.gcr.io/broad-gotc-prod/python@sha256:4182171bfe18c3e81d7d60bf200528d0ffb924239154f7cd93f167c99174ebe6 /cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CreateSequenceGroupingTSV/execution/script

    # get the return code (working even if the container was detached)
    rc=$(docker wait cat /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CreateSequenceGroupingTSV/execution/docker_cid)

    # remove the container after waiting
    docker rm cat /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CreateSequenceGroupingTSV/execution/docker_cid

    # return exit code
    exit $rc
    [2020-10-19 16:47:23,72] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.CreateSequenceGroupingTSV:NA:1]: job id: 322272
    [2020-10-19 16:47:23,72] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.GetBwaVersion:NA:1]: job id: 322249
    [2020-10-19 16:47:23,72] [info] df932bf3-282e-49dc-b3ff-f25779b589a5-SubWorkflowActor-SubWorkflow-UnmappedBamToAlignedBam:-1:1 [df932bf3]: Starting UnmappedBamToAlignedBam.CollectQualityYieldMetrics
    [2020-10-19 16:47:23,72] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.GetBwaVersion:NA:1]: Status change from - to WaitingForReturnCode
    [2020-10-19 16:47:23,72] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.CreateSequenceGroupingTSV:NA:1]: Status change from - to WaitingForReturnCode
    [2020-10-19 16:47:24,01] [info] Assigned new job execution tokens to the following groups: 439d021c: 1
    [2020-10-19 16:47:24,01] [warn] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.CollectQualityYieldMetrics:0:1]: Unrecognized runtime attribute keys: preemptible, disks, memory
    [2020-10-19 16:47:24,02] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.CollectQualityYieldMetrics:0:1]: java -Xms2000m -jar /usr/gitc/picard.jar \
    CollectQualityYieldMetrics \
    INPUT=/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CollectQualityYieldMetrics/shard-0/inputs/1286628295/H06HDADXX130110.1.ATCACGAT.20k.unmapped.bam \
    OQ=true \
    OUTPUT=H06HDADXX130110.1.ATCACGAT.20k.unmapped.unmapped.quality_yield_metrics
    [2020-10-19 16:47:24,02] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.CollectQualityYieldMetrics:0:1]: executing: # make sure there is no preexisting Docker CID file
    rm -f /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CollectQualityYieldMetrics/shard-0/execution/docker_cid
    # run as in the original configuration without --rm flag (will remove later)
    docker run \
    --cidfile /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CollectQualityYieldMetrics/shard-0/execution/docker_cid \
    -i \
    \
    --entrypoint /bin/bash \
    -v /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CollectQualityYieldMetrics/shard-0:/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CollectQualityYieldMetrics/shard-0:delegated \
    us.gcr.io/broad-gotc-prod/genomes-in-the-cloud@sha256:93ae8b895f4e83dfc20dd2651e87baccac7dd2cbe0af602bf50afcc4b9e6f925 /cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CollectQualityYieldMetrics/shard-0/execution/script

    # get the return code (working even if the container was detached)
    rc=$(docker wait cat /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CollectQualityYieldMetrics/shard-0/execution/docker_cid)

    # remove the container after waiting
    docker rm cat /home/makimenkova/gatk-workflows/cromwell-executions/WholeGenomeGermlineSingleSample/439d021c-71be-4340-a130-c2f750b174b1/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/df932bf3-282e-49dc-b3ff-f25779b589a5/call-CollectQualityYieldMetrics/shard-0/execution/docker_cid

    # return exit code
    exit $rc
    [2020-10-19 16:47:28,72] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.CollectQualityYieldMetrics:0:1]: job id: 322312
    [2020-10-19 16:47:28,72] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.CollectQualityYieldMetrics:0:1]: Status change from - to WaitingForReturnCode
    [2020-10-19 16:47:49,85] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.CollectQualityYieldMetrics:0:1]: Status change from WaitingForReturnCode to Done
    [2020-10-19 16:47:51,43] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.CreateSequenceGroupingTSV:NA:1]: Status change from WaitingForReturnCode to Done
    [2020-10-19 16:47:52,70] [info] BackgroundConfigAsyncJobExecutionActor [df932bf3UnmappedBamToAlignedBam.GetBwaVersion:NA:1]: Status change from WaitingForReturnCode to Done
    [2020-10-19 16:47:54,33] [info] df932bf3-282e-49dc-b3ff-f25779b589a5-SubWorkflowActor-SubWorkflow-UnmappedBamToAlignedBam:-1:1 [df932bf3]: Starting UnmappedBamToAlignedBam.SamToFastqAndBwaMemAndMba
    [2020-10-19 16:47:54,61] [info] Assigned new job execution tokens to the following groups: 439d021c: 1
    [2020-10-19 16:47:56,30] [info] WorkflowManagerActor Workflow 439d021c-71be-4340-a130-c2f750b174b1 failed (during ExecutingWorkflowState): cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1$$anon$1: Call input and runtime attributes evaluation failed for SamToFastqAndBwaMemAndMba:
    Failed to evaluate input 'disk_size' (reason 1 of 1): ValueEvaluator[IdentifierLookup]: No suitable input for 'bwa_ref_size' amongst {input_bam, bwa_version, bwa_commandline, output_bam_basename, reference_fasta, hard_clip_reads, compression_level, disk_multiplier, unmapped_bam_size, preemptible_tries, ref_size}
    Failed to evaluate input 'bwa_ref_size' (reason 1 of 1): [Attempted 1 time(s)] - NoSuchFileException: /home/makimenkova/gatk-workflows/inputs/Homo_sapiens_assembly38.fasta.64.alt
    at cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1.applyOrElse(JobPreparationActor.scala:81)
    at cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1.applyOrElse(JobPreparationActor.scala:74)
    at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:38)
    at akka.actor.FSM.processEvent(FSM.scala:804)
    at akka.actor.FSM.processEvent$(FSM.scala:801)
    at cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor.processEvent(JobPreparationActor.scala:46)
    at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:798)
    at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:793)
    at akka.actor.Actor.aroundReceive(Actor.scala:537)
    at akka.actor.Actor.aroundReceive$(Actor.scala:535)
    at cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor.aroundReceive(JobPreparationActor.scala:46)
    at akka.actor.ActorCell.receiveMessage(ActorCell.scala:577)
    at akka.actor.ActorCell.invoke(ActorCell.scala:547)
    at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:270)
    at akka.dispatch.Mailbox.run(Mailbox.scala:231)
    at akka.dispatch.Mailbox.exec(Mailbox.scala:243)
    at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
    at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
    at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
    at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:175)

    [2020-10-19 16:47:56,30] [info] WorkflowManagerActor WorkflowActor-439d021c-71be-4340-a130-c2f750b174b1 is in a terminal state: WorkflowFailedState
    [2020-10-19 16:48:05,79] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
    [2020-10-19 16:48:08,87] [info] Workflow polling stopped
    [2020-10-19 16:48:08,87] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
    [2020-10-19 16:48:08,87] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
    [2020-10-19 16:48:08,88] [info] JobExecutionTokenDispenser stopped
    [2020-10-19 16:48:08,88] [info] WorkflowLogCopyRouter stopped
    [2020-10-19 16:48:08,88] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
    [2020-10-19 16:48:08,88] [info] 0 workflows released by cromid-8a2ac52
    [2020-10-19 16:48:08,88] [info] Aborting all running workflows.
    [2020-10-19 16:48:08,88] [info] WorkflowStoreActor stopped
    [2020-10-19 16:48:08,88] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
    [2020-10-19 16:48:08,88] [info] WorkflowManagerActor All workflows finished
    [2020-10-19 16:48:08,88] [info] WorkflowManagerActor stopped
    [2020-10-19 16:48:09,00] [info] Connection pools shut down
    [2020-10-19 16:48:09,00] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
    [2020-10-19 16:48:09,00] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
    [2020-10-19 16:48:09,00] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
    [2020-10-19 16:48:09,00] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
    [2020-10-19 16:48:09,00] [info] SubWorkflowStoreActor stopped
    [2020-10-19 16:48:09,00] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
    [2020-10-19 16:48:09,00] [info] Shutting down IoProxy - Timeout = 1800 seconds
    [2020-10-19 16:48:09,00] [info] JobStoreActor stopped
    [2020-10-19 16:48:09,00] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
    [2020-10-19 16:48:09,00] [info] DockerHashActor stopped
    [2020-10-19 16:48:09,00] [info] CallCacheWriteActor stopped
    [2020-10-19 16:48:09,00] [info] KvWriteActor Shutting down: 0 queued messages to process
    [2020-10-19 16:48:09,00] [info] WriteMetadataActor Shutting down: 0 queued messages to process
    [2020-10-19 16:48:09,00] [info] IoProxy stopped
    [2020-10-19 16:48:09,00] [info] ServiceRegistryActor stopped
    [2020-10-19 16:48:09,01] [info] Shutting down connection pool: curAllocated=2 idleQueues.size=1 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
    [2020-10-19 16:48:09,01] [info] Shutting down connection pool: curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
    [2020-10-19 16:48:09,01] [info] Shutting down connection pool: curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
    [2020-10-19 16:48:09,01] [info] Shutting down connection pool: curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
    [2020-10-19 16:48:09,02] [info] Database closed
    [2020-10-19 16:48:09,02] [info] Stream materializer shut down
    [2020-10-19 16:48:09,02] [info] WDL HTTP import resolver closed
    Workflow 439d021c-71be-4340-a130-c2f750b174b1 transitioned to state Failed
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    Beri Shifaw
    Failed to evaluate input 'disk_size' (reason 1 of 1): ValueEvaluator[IdentifierLookup]: No suitable input for 'bwa_ref_size' amongst {input_bam, bwa_version, bwa_commandline, output_bam_basename, reference_fasta, hard_clip_reads, compression_level, disk_multiplier, unmapped_bam_size, preemptible_tries, ref_size}
    Failed to evaluate input 'bwa_ref_size' (reason 1 of 1): [Attempted 1 time(s)] - NoSuchFileException: /home/makimenkova/gatk-workflows/inputs/Homo_sapiens_assembly38.fasta.64.alt
    at cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1.applyOrElse(JobPreparationActor.scala:81)

    Looks like its having trouble finding one of the files, can you confirm that /home/makimenkova/gatk-workflows/inputs/Homo_sapiens_assembly38.fasta.64.alt exist in that directory. 

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    Maria Akimenkova

    Thanks for the answer! Sorry to bother you, the interface is still a little tricky for me. I checked and corrected the file names again.

    [First 300 bytes]:[E::bwa_idx_load_from_disk] fail to locate the index files

    The content of the stderr: https://drive.google.com/file/d/1RmnUBMyiCjgZHUEKomvBQK_xmGvs8mrL/view?usp=sharing

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    Beri Shifaw

    Do you have a bam index file in the same directory as 

    /home/makimenkova/gatk-workflows/inputs/NA12878_20k/H06HDADXX130110.1.ATCACGAT.20k.unmapped.bam
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    Maria Akimenkova

    Yes, the .bai file in the same directory

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    Beri Shifaw

    From the error message: "[E::bwa_idx_load_from_disk] fail to locate the index files
    I think it's having trouble accessing one of your files."

    From the error message: "Exception in thread "main" htsjdk.samtools.SAMException: Error in writing fastq file /dev/stdout"
    I think its related to your reference files

    Try placing all the fasta associated files in one directory (/home/makimenkova/gatk-workflows/inputs/reference/) and updating your json

     

    "reference_fasta": {
          "ref_dict": "/home/makimenkova/gatk-workflows/inputs/reference/Homo_sapiens_assembly38.dict",
          "ref_fasta": "/home/makimenkova/gatk-workflows/inputs/reference/Homo_sapiens_assembly38.fasta",
          "ref_fasta_index": "/home/makimenkova/gatk-workflows/inputs/reference/Homo_sapiens_assembly38.fasta.fai",
          "ref_alt": "/home/makimenkova/gatk-workflows/inputs/Homo_sapiens_assembly38.fasta.64.alt",
          "ref_sa": "/home/makimenkova/gatk-workflows/inputs/Homo_sapiens_assembly38.fasta.64.sa",
          "ref_amb": "/home/makimenkova/gatk-workflows/inputs/Homo_sapiens_assembly38.fasta.64.amb",
          "ref_bwt": "/home/makimenkova/gatk-workflows/inputs/Homo_sapiens_assembly38.fasta.64.bwt",
          "ref_ann": "/home/makimenkova/gatk-workflows/inputs/Homo_sapiens_assembly38.fasta.64.ann",
          "ref_pac": "/home/makimenkova/gatk-workflows/inputs/Homo_sapiens_assembly38.fasta.64.pac"
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