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An error in preprocessing pipeline

suimyesuimye TokyoMember

Hi,
I am now trying to use preprocessing pipline for getting clean mapped BAM. I have excused best practice pipeline "processing-for-variant-discovery-gatk4.wdl" and got error message described below.

java -jar ~/bin/cromwell-36.1.jar run /home/masaki.morioka/project/test/processing-for-variant-discovery-gatk4.wdl -i /home/masaki.morioka/project/test/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json >test.log 2>&1

[2019-02-28 04:32:08,39] [error] WorkflowManagerActor Workflow c12efd4e-a08b-42e2-bf6a-06db0721f1bb failed (during ExecutingWorkflowState): Job PreProcessingForVariantDiscovery_GATK4.MergeBamAlignment:0:1 exited with return code 127 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /home/masaki.morioka/project/test/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/c12efd4e-a08b-42e2-bf6a-06db0721f1bb/call-MergeBamAlignment/shard-0/execution/stderr.
 /cromwell-executions/PreProcessingForVariantDiscovery_GATK4/c12efd4e-a08b-42e2-bf6a-06db0721f1bb/call-MergeBamAlignment/shard-0/execution/script: line 24: /masaki.morioka/tool/gatk-4.0.6.0/gatk: No such file or directory

It looks like a very simple matter. But I have never resolved this error. When I have excused GATK by copying this path, GATK has correctly worked as,

:~/project/test$ /home/masaki.morioka/tool/gatk-4.0.6.0/gatk

 Usage template for all tools (uses --spark-runner LOCAL when used with a Spark tool)
    gatk AnyTool toolArgs

 Usage template for Spark tools (will NOT work on non-Spark tools)
    gatk SparkTool toolArgs  [ -- --spark-runner <LOCAL | SPARK | GCS> sparkArgs ]

 Getting help
    gatk --list       Print the list of available tools

    gatk Tool --help  Print help on a particular tool

 Configuration File Specification
     --gatk-config-file                PATH/TO/GATK/PROPERTIES/FILE

 gatk forwards commands to GATK and adds some sugar for submitting spark jobs

   --spark-runner <target>    controls how spark tools are run
     valid targets are:
     LOCAL:      run using the in-memory spark runner
     SPARK:      run using spark-submit on an existing cluster 
                 --spark-master must be specified
                 --spark-submit-command may be specified to control the Spark submit command
                 arguments to spark-submit may optionally be specified after -- 
     GCS:        run using Google cloud dataproc
                 commands after the -- will be passed to dataproc
                 --cluster <your-cluster> must be specified after the --
                 spark properties and some common spark-submit parameters will be translated 
                 to dataproc equivalents

   --dry-run      may be specified to output the generated command line without running it
   --java-options 'OPTION1[ OPTION2=Y ... ]'   optional - pass the given string of options to the 
                 java JVM at runtime.  
                 Java options MUST be passed inside a single string with space-separated values.

In Json file, I have written the gatk path as,

String gatk_path = select_first([gatk_path_override, "/home/masaki.morioka/tool/gatk-4.0.6.0/gatk"])

Do you have any suggestion for this?

My environment is

cromwell v36
gatk v4.0.6.0

Answers

  • suimyesuimye TokyoMember

    gatk command-line was executed from

    /cromwell-executions/PreProcessingForVariantDiscovery_GATK4/c12efd4e-a08b-42e2-bf6a-06db0721f1bb/call-MergeBamAlignment/shard-0/execution/script

    .
    In this script file, gatk command-line was written in line 24.

    /home/masaki.morioka/tool/gatk-4.0.6.0/gatk --java-options "-Dsamjdk.compression_level=5 -Xms3000m" \
      MergeBamAlignment \
      --VALIDATION_STRINGENCY SILENT \
      --EXPECTED_ORIENTATIONS FR \
      --ATTRIBUTES_TO_RETAIN X0 \
      --ALIGNED_BAM /cromwell-executions/PreProcessingForVariantDiscovery_GATK4/c17797f1-0a7e-47d7-b95b-b16156c9c0fd/call-MergeBamAlignment/shard-0/inputs/456039380/6484.unmerged.bam \
      --UNMAPPED_BAM ./cromwell-executions/PreProcessingForVariantDiscovery_GATK4/c17797f1-0a7e-47d7-b95b-b16156c9c0fd/call-MergeBamAlignment/shard-0/inputs/1382697050/6484.bam \
      --OUTPUT 6484.aligned.unsorted.bam \
      --REFERENCE_SEQUENCE /cromwell-executions/PreProcessingForVariantDiscovery_GATK4/c17797f1-0a7e-47d7-b95b-b16156c9c0fd/call-MergeBamAlignment/shard-0/inputs/-960734774/Homo_sapiens_assembly38.fasta \
      --PAIRED_RUN true \
      --SORT_ORDER "unsorted" \
      --IS_BISULFITE_SEQUENCE false \
      --ALIGNED_READS_ONLY false \
      --CLIP_ADAPTERS false \
      --MAX_RECORDS_IN_RAM 2000000 \
      --ADD_MATE_CIGAR true \
      --MAX_INSERTIONS_OR_DELETIONS -1 \
      --PRIMARY_ALIGNMENT_STRATEGY MostDistant \
      --PROGRAM_RECORD_ID "bwamem" \
      --PROGRAM_GROUP_VERSION "0.7.15-r1140" \
      --PROGRAM_GROUP_COMMAND_LINE "bwa mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta" \
      --PROGRAM_GROUP_NAME "bwamem" \
      --UNMAPPED_READ_STRATEGY COPY_TO_TAG \
      --ALIGNER_PROPER_PAIR_FLAGS true \
      --UNMAP_CONTAMINANT_READS true
    )  > "$outc17797f1" 2> "$errc17797f1"
    echo $? > /cromwell-executions/PreProcessingForVariantDiscovery_GATK4/c17797f1-0a7e-47d7-b95b-b16156c9c0fd/call-MergeBamAlignment/shard-0/execution/rc.tmp
    

    It seems that this command did not work as "No such file or directory".

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