Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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    This is the result of GenomicsDBImport

    -[ 201] callset.json
    -[4.0K] chr22$1$50818468
    |-[4.0K] __3d7b0c29-9d8b-4748-a08a-c1e0a9136cf647572466251520_1590412882146
    ||-[133K] AD.tdb
    ||-[ 54K] AD_var.tdb
    ||-[3.2M] ALT.tdb
    ||-[ 77K] ALT_var.tdb
    ||-[ 85K] BaseQRankSum.tdb
    ||-[192K] __book_keeping.tdb.gz
    ||-[4.1M] __coords.tdb
    ||-[1011K] DP_FORMAT.tdb
    ||-[114K] DP.tdb
    ||-[3.5M] END.tdb
    ||-[108K] ExcessHet.tdb
    ||-[ 64K] FILTER.tdb
    ||-[ 0] FILTER_var.tdb
    ||-[1.1M] GQ.tdb
    ||-[2.9M] GT.tdb
    ||-[120K] GT_var.tdb
    ||-[ 64K] ID.tdb
    ||-[ 0] ID_var.tdb
    ||-[ 64K] InbreedingCoeff.tdb
    ||-[1.0M] MIN_DP.tdb
    ||-[128K] MLEAC.tdb
    ||-[ 32K] MLEAC_var.tdb
    ||-[128K] MLEAF.tdb
    ||-[ 36K] MLEAF_var.tdb
    ||-[ 82K] MQRankSum.tdb
    ||-[ 98K] PGT.tdb
    ||-[5.8K] PGT_var.tdb
    ||-[ 99K] PID.tdb
    ||-[ 15K] PID_var.tdb
    ||-[2.9M] PL.tdb
    ||-[3.5M] PL_var.tdb
    ||-[ 77K] PS.tdb
    ||-[143K] QUAL.tdb
    ||-[163K] RAW_MQandDP.tdb
    ||-[ 84K] ReadPosRankSum.tdb
    ||-[3.2M] REF.tdb
    ||-[655K] REF_var.tdb
    ||-[174K] SB.tdb
    ||-[ 0] __tiledb_fragment.tdb
    |-[ 535] __array_schema.tdb
    |-[4.0K] genomicsdb_meta_dir
    | -[ 60] genomicsdb_meta_a793298a-95f2-475e-b10b-726695483e3a.json
    -[ 0] __tiledb_workspace.tdb
    -[ 33K] vcfheader.vcf
    -[ 39K] vidmap.json

    Thanks in advance.

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    Bhanu Gandham

    Can you try setting this environment variable and see if that solves the issue?


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    Hi,Bhanu! Is the command I entered like this:

    TILEDB_DISABLE_FILE_LOCKING=1 gatk GenomicsDBImport -V SRR630877.erc.g.vcf -V SRR630496.erc.g.vcf \
    --genomicsdb-workspace-path my_database --intervals chr22

    If yes, it will still produce the same error。

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    And I checked my environment variable, the parameter is displayed as ' declare -x TILEDB_DISABLE_FILE_LOCKING="1" '

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    Bhanu Gandham

    Hi hjwang


    Take a look at this thread, a similar issue was resolved here:

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    Bhanu Gandham

    Hi hjwang


    We think this is a NFS related issue. The workaround for this is to set env variable TILEDB_DISABLE_FILE_LOCKING=1 in the GenotypeGVCF step as well. This is something we are looking to fix in the future. 

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