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FastqToSam "No value found for tagged argument" for ISO 8601 --RUN_DATE parameter

FPBarthelFPBarthel HoustonMember

I am using FastqToSam to convert paired FQ files to uBAM as follows:

gatk --java-options {java_opt} FastqToSam \
            --FASTQ={R1} \
            --FASTQ2={R2} \
            --OUTPUT={output} \
            --READ_GROUP_NAME={RGID} \
            --PLATFORM_UNIT={RGPU} \
            --SAMPLE_NAME={RGSM} \
            --PLATFORM={RGPL} \
            --LIBRARY_NAME={RGLB} \
            --SEQUENCING_CENTER={RGCN} \
            --RUN_DATE={RGDT} \
            --SORT_ORDER=queryname

When I include the --RUN_DATE parameter (in my test I tried with 2011-04-30T01:00:00+0100) and I get the following error message: No value found for tagged argument: RUN_DATE=2011-04-30T01:00:00+0100. I have confirmed the string is a valid ISO 8601 date using the following tool. Running the exact same FastqToSam command without the --RUN_DATE parameter works without issues. Any reason for this error that I am missing?

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  • FPBarthelFPBarthel HoustonMember

    Any thoughts on this? I believe I am providing the correct input here for this parameter according to its description:

    --RUN_DATE,-DT:Iso8601Date    Date the run was produced, to insert into the read group header  Default value: null. 
    

    I have tried supplying the ISO 8601 with and without quotations and both led to the error above.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @FPBarthel
    Hi,

    Which version of GATK4 are you using? Can you try with the latest version of standalone Picard?

    Thanks,
    Sheila

  • FPBarthelFPBarthel HoustonMember

    Sure thing. Standalone Picard works fine (not sure if this is the latest version, but I had this version at hand).

    Using GATK 4.0.2.1

    gatk FastqToSam --FASTQ=test_R1.fq --FASTQ2=test_R2.fq --RUN_DATE=2011-04-30T01:00:00+0100 --OUTPUT=test.bam --SM=test
    

    Gives the error No value found for tagged argument: RUN_DATE=2011-04-30T01:00:00+0100

    Using Picard 2.18.1-SNAPSHOT

    java -jar XXXX/build/libs/picard.jar FastqToSam FASTQ=test_R1.fq FASTQ2=test_R2.fq RUN_DATE=2011-04-30T01:00:00+0100 OUTPUT=test.bam SM=test
    

    Works without issues

  • FPBarthelFPBarthel HoustonMember

    Unfortunately, this error still exists in gatk-4.0.5.1. Will this be fixed on next release?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @FPBarthel
    Hi,

    Sorry about that. I need to confirm with the team and get back to you.

    -Sheila

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited June 26

    @FPBarthel
    Hi again,

    It seems I was wrong and that the latest Picard release is not "pulled in" every time GATK is released. I am confirming with the team when this will happen next.

    -Sheila

    EDIT: It should go in tomorrow. https://github.com/broadinstitute/gatk/pull/4949

  • FPBarthelFPBarthel HoustonMember
    edited September 6

    Just to update on this issue with GATK 4.0.8.1. I found that this bug still exists at least when using AddOrReplaceReadgroups. I did not test FastqToSam here but I assume both are using the same Isodate parsing method?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @FPBarthel
    Hi,

    Hmm. Let me ask the team.

    -Sheila

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @FPBarthel
    Hi again,

    It seems the team has opened a new issue for this here.

    -Sheila

  • FPBarthelFPBarthel HoustonMember
    edited October 17

    Just tested this and confirmed that it works when dropping the "=" (using gatk 4.0.10.1). With the = it still doesn't work (perhaps the error message here could be more informative?). Thanks for the great detective work @cnorman, and apologies for the late reply.

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