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CombineVariants

Dear all,

I try to use the CombineVariants to combine about 200 samples like this:

java -Xmx30g -jar GenomeAnalysisTK.jar -R N.tab.all.fa -T CombineVariants --variant S046.vcf --variant S237.vcf --variant S129.vcf --variant S126.vcf --variant S209.vcf --variant S193.vcf --variant S158.vcf --variant S174.vcf --variant S001.vcf.idx --variant S135.vcf --variant S222.vcf --variant S101.vcf --variant S009.vcf --variant S143.vcf --variant S232.vcf --variant S206.vcf --variant S207.vcf --variant S210.vcf --variant S039.vcf --variant S072.vcf --variant S231.vcf --variant S133.vcf --variant S137.vcf --variant S139.vcf --variant S081.vcf --variant S246.vcf --variant S224.vcf --variant S121.vcf --variant S055.vcf --variant S114.vcf --variant S175.vcf --variant S131.vcf --variant S238.vcf --variant S060.vcf --variant S090.vcf --variant S053.vcf --variant S177.vcf --variant S185.vcf --variant S202.vcf --variant S240.vcf --variant S025.vcf --variant S031.vcf --variant S250.vcf --variant S227.vcf --variant S223.vcf --variant S155.vcf --variant S235.vcf --variant S024.vcf --variant S014.vcf --variant S243.vcf --variant S056.vcf --variant S144.vcf --variant S136.vcf --variant S033.vcf --variant S005.vcf --variant S059.vcf --variant S047.vcf --variant S122.vcf --variant S084.vcf --variant S119.vcf --variant S216.vcf --variant S023.vcf --variant S028.vcf --variant S016.vcf --variant S219.vcf --variant S061.vcf --variant S088.vcf --variant S248.vcf --variant S196.vcf --variant S094.vcf --variant S186.vcf --variant S204.vcf --variant S075.vcf --variant S205.vcf --variant S079.vcf --variant S029.vcf --variant S161.vcf --variant S140.vcf --variant S096.vcf --variant S117.vcf --variant S118.vcf --variant S150.vcf --variant S097.vcf --variant S148.vcf --variant S153.vcf --variant S178.vcf --variant S040.vcf --variant S063.vcf --variant S099.vcf --variant S179.vcf --variant S073.vcf --variant S168.vcf --variant S154.vcf --variant S230.vcf --variant S213.vcf --variant S057.vcf --variant S098.vcf --variant S247.vcf --variant S244.vcf --variant S228.vcf --variant S242.vcf --variant S002.vcf.idx --variant S054.vcf --variant S008.vcf --variant S087.vcf --variant S199.vcf --variant S108.vcf --variant S019.vcf --variant S241.vcf --variant S006.vcf --variant S208.vcf --variant S212.vcf --variant S080.vcf --variant S187.vcf --variant S123.vcf --variant S043.vcf --variant S163.vcf --variant S124.vcf --variant S183.vcf --variant S049.vcf --variant S038.vcf --variant S149.vcf --variant S036.vcf --variant S211.vcf --variant S157.vcf --variant S142.vcf --variant S184.vcf --variant S078.vcf --variant S085.vcf --variant S050.vcf --variant S091.vcf --variant S176.vcf --variant S214.vcf --variant S215.vcf --variant S083.vcf --variant S062.vcf --variant S065.vcf --variant S032.vcf --variant S125.vcf --variant S156.vcf --variant S182.vcf --variant S086.vcf --variant S255.vcf --variant S254.vcf --variant S001.vcf --variant S162.vcf --variant S181.vcf --variant S192.vcf --variant S169.vcf --variant S074.vcf --variant S173.vcf --variant S042.vcf --variant S106.vcf --variant S003.vcf --variant S207_supp.vcf --variant S071.vcf --variant S2.vcf --variant S035.vcf --variant S037.vcf --variant S127.vcf --variant S165.vcf --variant S170.vcf --variant S027.vcf --variant S141.vcf --variant S252.vcf --variant S234.vcf --variant S191.vcf --variant S197.vcf --variant S147.vcf --variant S058.vcf --variant S172.vcf --variant S010.vcf --variant S138.vcf --variant S066.vcf --variant S041.vcf --variant S082.vcf --variant S171.vcf --variant S132.vcf --variant S015.vcf --variant S200.vcf --variant S069.vcf --variant S220.vcf --variant S218.vcf --variant S076.vcf --variant S134.vcf --variant S151.vcf --variant S130.vcf --variant S221.vcf --variant S120.vcf --variant S145.vcf --variant S011.vcf --variant S217.vcf --variant S159.vcf --variant S067.vcf --variant S021.vcf --variant S020.vcf --variant S104.vcf --variant S128.vcf --variant S253.vcf --variant S225.vcf --variant S107.vcf --variant S201.vcf --variant S034.vcf --variant S203.vcf --variant S116.vcf --variant S167.vcf --variant S115.vcf --variant S002.vcf --variant S003.vcf.idx --variant S064.vcf --variant S012.vcf --variant S111.vcf --variant S017.vcf --variant S189.vcf --variant S236.vcf --variant S070.vcf --variant S113.vcf --variant S007.vcf --variant S112.vcf --variant S018.vcf --variant S229.vcf --variant S245.vcf --variant S093.vcf --variant S251.vcf --variant S166.vcf --variant S164.vcf --variant S239.vcf --variant S030.vcf --variant S004.vcf --variant S095.vcf --variant S110.vcf --variant S188.vcf --variant S109.vcf --variant S013.vcf --variant S051.vcf --variant S100.vcf --variant S194.vcf --variant S160.vcf --variant S190.vcf --variant S105.vcf --variant S146.vcf --variant S198.vcf --variant S092.vcf --variant S044.vcf --variant S052.vcf --variant S026.vcf --variant S249.vcf --variant S180.vcf --variant S103.vcf --variant S022.vcf --variant S089.vcf --variant S102.vcf --variant S077.vcf --variant S068.vcf --variant S048.vcf --variant S195.vcf --variant S152.vcf --variant S045.vcf --variant S226.vcf -o output_SNP.vcf -genotypeMergeOptions UNIQUIFY

However, there always some error message:

INFO 05:05:38,893 HelpFormatter - --------------------------------------------------------------------------------
INFO 05:05:38,893 HelpFormatter - --------------------------------------------------------------------------------
INFO 05:05:39,871 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
ERROR Name FeatureType Documentation
ERROR BCF2 VariantContext (this is an external codec and is not documented within GATK)
ERROR VCF VariantContext (this is an external codec and is not documented within GATK)
ERROR VCF3 VariantContext (this is an external codec and is not documented within GATK)
ERROR ------------------------------------------------------------------------------------------

Can anyone give me some suggestions?

Jingjing

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Best Answer

Answers

  • jjjscuedujjjscuedu Member

    Thanks a lot for your help.

    Another questions is how many vcf file do this command support, because I have another error message now:

    WARN 19:17:21,212 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file S117.vcf.idx because you already have a lock on t
    his file.
    INFO 19:17:21,213 RMDTrackBuilder - Could not acquire a shared lock on index file S117.vcf.idx, falling back to using an in-memory inde
    x for this GATK run.
    INFO 19:19:08,655 ProgressMeter - Chr01:14995145 162133.0 24.3 m 2.5 h 0.3% 5.0 d 4.9 d

    ERROR ------------------------------------------------------------------------------------------
    ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
    ERROR
    ERROR This means that one or more arguments or inputs in your command are incorrect.
    ERROR The error message below tells you what is the problem.
    ERROR
    ERROR If the problem is an invalid argument, please check the online documentation guide
    ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ERROR
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ERROR
    ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    ERROR
    ERROR MESSAGE: Timeout of 30000 milliseconds was reached while trying to acquire a lock on file S117.vcf.idx. Since the GATK uses

    non-blocking lock acquisition calls that are not supposed to wait, this implies a problem with the file locking support in your operating system.

    ERROR ------------------------------------------------------------------------------------------

    It seems the number of locking in my server is not enough?

    Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    Please try using --disable_auto_index_creation_and_locking_when_reading_rods in your command line and let me know if that solves the issue.

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