GENOMICSDB_TIMER meaning while doing GenotypeGVCFs

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Gongyuan Cao

• March 17, 2024 15:56

Hi all,

I was calling variants from a rather large dataset and encountered this output for the first time. I wonder if this is normal or if it indicates that something is skipped due to CPU limit.

Thanks,

Gongyuan

module load GATK/4.1.9.0

 

 

java -jar -Xms390g $GATK GenotypeGVCFs \

        -V gendb:///DBwork1/ \

        -R final.fasta \

        -O 2018_WGS_5099_1.vcf.gz \

        --genomicsdb-shared-posixfs-optimizations \

        -L picard.interval_list

output:

00:04:57.667 INFO  ProgressMeter -        CHR10:1044381             49.6                982000          19797.2

00:05:08.131 INFO  ProgressMeter -        CHR10:1061535             49.8                999000          20069.4

GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),820.2335175789718,Cpu time(s),155.23975346400007

GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),5.8576E-5,Cpu time(s),5.7426E-5

GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),6.1236E-5,Cpu time(s),6.0924E-5

GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),6.2381E-5,Cpu time(s),6.125E-5

GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),6.1884E-5,Cpu time(s),6.0515E-5

GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),6.245E-5,Cpu time(s),6.0747E-5

GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),5.8853E-5,Cpu time(s),5.0143E-5

00:12:58.828 INFO  ProgressMeter -        CHR10:1094768             57.6               1003000          17406.4

00:13:09.178 INFO  ProgressMeter -        CHR10:1115282             57.8               1021000          17665.9

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• 

  David Roazen

  • March 18, 2024 17:28

  Hi Gongyuan Cao,

  This message is no cause for concern. It just indicates that a GenomicsDB operation took slightly longer than usual, but otherwise completed normally.

  Regards,

  David

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• 

  Gongyuan Cao

  • March 18, 2024 17:37

  Thanks David! That is a relief. It might be easier for both users and developers if this kind of explanation can be included in the manuals in the future.

  Regards,

  Gongyuan

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