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Running GenomicsDBImport: stuck on 'INFO GenomicsDBImport - Importing batch 1 with 62 samples'


I am running GenomicsDBImport on 62 human exome data and somehow the process stuck in the very beginning of the process. Please see below message:

16:24:19.150 INFO  ProgressMeter - Starting traversal
16:24:19.150 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Batches Processed   Batches/Minute
16:24:19.378 INFO  GenomicsDBImport - Starting batch input file preload
16:24:36.900 INFO  GenomicsDBImport - Finished batch preload
16:24:36.900 INFO  GenomicsDBImport - Importing batch 1 with 62 samples

It stucks right here for several hours.

Here is the command I used:

java -jar $GATK GenomicsDBImport -R $hg19 \
     --sampleNameMap sample.map
     -L chr1 \
     --genomicsdb-workspace-path $output

I wonder if this is normal. Thank you for your help in advance!



  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @masaki396

    Are you still facing this issue? If yes, would you please show me what your sample.map looks like? Please note: Using vcfs with incompatible headers may result in silent data corruption.

  • wbsimeywbsimey California Academy of SciencesMember ✭✭

    I have the very same experience, but I hit ENTER and it instantly completed. I had been waiting for almost two weeks before I decided to hit ENTER. Now I hit ENTER right away to preload this user input and this works for me.
    I am using v4.1.2.0 via conda. I have not tried with my Docker instance. I noticed the latest version is I will update and try again.

    my command was:

    gatk --java-options "-Xmx200g -Xms200g" \
        GenomicsDBImport \
        --genomicsdb-workspace-path ../Tse_scaff_4_database \
        -L scaffold_4 \
        --sample-name-map ../gVCFs/scaffold_4_sample_names_map.txt \
        --tmp-dir=/data/tmp \
        --reader-threads 8
  • wbsimeywbsimey California Academy of SciencesMember ✭✭

    I reran the same script as above with v4.1.3.0, but with a different interval, and it completed on its own without any user input.

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