combine GVCF
Answered
REQUIRED for all errors and issues:
a) GATK version used:
ml biocontainers gatk4/4.2.5.0
b) Exact command used:
gatk CombineGVCFs \
-R persian_walnut_junglans_regia_chrs_sept18.fasta \
--variant SRR11497836.vcf.gz \
--variant SRR11497835.vcf.gz \
--variant SRR11497834.vcf.gz \
--variant SRR11497833.vcf.gz \
--variant SRR11497832.vcf.gz \
--variant SRR11497831.vcf.gz \
--variant SRR11497830.vcf.gz \
--variant SRR11497829.vcf.gz \
--variant SRR11497828.vcf.gz \
--variant SRR11497827.vcf.gz \
--variant SRR11497826.vcf.gz \
......continued
c) Entire program log:
Using GATK jar /usr/local/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /usr/local/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar CombineGVCFs -R persian_walnut_junglans_regia_chrs_sept18.fasta --variant SRR11497836.vcf.gz --variant SRR11497835.vcf.gz --variant SRR11497834.vcf.gz --variant SRR11497833.vcf.gz --variant SRR11497832.vcf.gz --variant SRR11497831.vcf.gz --variant SRR11497830.vcf.gz --variant SRR11497829.vcf.gz --variant SRR11497828.vcf.gz --variant SRR11497827.vcf.gz --variant SRR11497826.vcf.gz --variant SRR11497825.vcf.gz --variant SRR11497824.vcf.gz --variant SRR11497823.vcf.gz --variant SRR11497822.vcf.gz --variant SRR11497821.vcf.gz --variant SRR11497820.vcf.gz --variant SRR11497819.vcf.gz --variant SRR11497818.vcf.gz --variant SRR11497817.vcf.gz --variant SRR11497816.vcf.gz --variant SRR11497815.vcf.gz --variant SRR11497814.vcf.gz --variant SRR11497813.vcf.gz --variant SRR11497812.vcf.gz --variant SRR11497811.vcf.gz --variant SRR11497810.vcf.gz --variant SRR11497809.vcf.gz --variant SRR11497808.vcf.gz --variant SRR11497807.vcf.gz --variant SRR11497806.vcf.gz --variant SRR11497805.vcf.gz --variant SRR11497804.vcf.gz --variant SRR11497803.vcf.gz --variant SRR11497802.vcf.gz --variant SRR11497800.vcf.gz --variant SRR11497799.vcf.gz --variant SRR11497798.vcf.gz --variant SRR11497797.vcf.gz --variant SRR11497796.vcf.gz --variant SRR11497795.vcf.gz --variant SRR11497794.vcf.gz --variant SRR11497793.vcf.gz --variant SRR11497792.vcf.gz --variant SRR11497790.vcf.gz --variant SRR11497791.vcf.gz --variant SRR11497789.vcf.gz --variant SRR11497788.vcf.gz --variant SRR11497787.vcf.gz --variant SRR11497786.vcf.gz --variant SRR11497785.vcf.gz --variant SRR11497783.vcf.gz --variant SRR11497784.vcf.gz --variant SRR11497782.vcf.gz --variant SRR11497781.vcf.gz --variant SRR11497780.vcf.gz --variant SRR11497779.vcf.gz --variant SRR11497778.vcf.gz --variant SRR11497777.vcf.gz --variant SRR11497776.vcf.gz --variant SRR11497775.vcf.gz --variant SRR11497774.vcf.gz --variant SRR11497773.vcf.gz --variant SRR11497772.vcf.gz --variant SRR8772786.vcf.gz --variant SRR6804856.vcf.gz --variant SRR6804855.vcf.gz --variant SRR6804854.vcf.gz --variant SRR6804853.vcf.gz --variant SRR6804852.vcf.gz --variant SRR6804851.vcf.gz --variant SRR6804850.vcf.gz --variant SRR6804849.vcf.gz --variant SRR6804848.vcf.gz --variant SRR6804847.vcf.gz --variant SRR6804846.vcf.gz --variant SRR6804845.vcf.gz --variant SRR6804843.vcf.gz --variant SRR6804842.vcf.gz --variant SRR6804841.vcf.gz --variant SRR6804840.vcf.gz --variant SRR6793981.vcf.gz --variant SRR6793980.vcf.gz --variant SRR6793979.vcf.gz --variant SRR6793978.vcf.gz --variant SRR6793977.vcf.gz --variant SRR6793976.vcf.gz --variant SRR6793975.vcf.gz --variant SRR6793974.vcf.gz --variant SRR6793973.vcf.gz --variant SRR6793972.vcf.gz --variant SRR6793971.vcf.gz --variant SRR6793970.vcf.gz --variant SRR6793969.vcf.gz --variant SRR6793968.vcf.gz --variant SRR6793967.vcf.gz --variant SRR6793966.vcf.gz --variant SRR6793965.vcf.gz --variant SRR14085898.vcf.gz --variant SRR13361464.vcf.gz --variant SRR13361463.vcf.gz --variant Cmy_IYBZ.vcf.gz --variant Cmy_IXLR.vcf.gz --variant Cmy_IXLQ.vcf.gz --variant Cilli.vcf.gz --variant Ccord_IXSD.vcf.gz --variant Ccord_IXIH.vcf.gz --variant Caqu.vcf -O all_carya_wg.vcf.gz
18:54:13.114 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Mar 11, 2022 6:54:13 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
18:54:13.327 INFO CombineGVCFs - ------------------------------------------------------------
18:54:13.328 INFO CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.2.5.0
18:54:13.328 INFO CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
18:54:13.328 INFO CombineGVCFs - Executing as aebrahi@brown-a009.rcac.purdue.edu on Linux v3.10.0-1062.9.1.el7.x86_64 amd64
18:54:13.328 INFO CombineGVCFs - Java runtime: OpenJDK 64-Bit Server VM v11.0.9.1-internal+0-adhoc..src
18:54:13.329 INFO CombineGVCFs - Start Date/Time: March 11, 2022 at 6:54:13 PM GMT
18:54:13.329 INFO CombineGVCFs - ------------------------------------------------------------
18:54:13.329 INFO CombineGVCFs - ------------------------------------------------------------
18:54:13.330 INFO CombineGVCFs - HTSJDK Version: 2.24.1
18:54:13.330 INFO CombineGVCFs - Picard Version: 2.25.4
18:54:13.330 INFO CombineGVCFs - Built for Spark Version: 2.4.5
18:54:13.330 INFO CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:54:13.330 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:54:13.330 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:54:13.330 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:54:13.330 INFO CombineGVCFs - Deflater: IntelDeflater
18:54:13.331 INFO CombineGVCFs - Inflater: IntelInflater
18:54:13.331 INFO CombineGVCFs - GCS max retries/reopens: 20
18:54:13.331 INFO CombineGVCFs - Requester pays: disabled
18:54:13.331 INFO CombineGVCFs - Initializing engine
18:54:13.461 INFO CombineGVCFs - Shutting down engine
[March 11, 2022 at 6:54:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1879048192
***********************************************************************
A USER ERROR has occurred: Couldn't read file file:///scratch/brown/aebrahi/regia_ref2/carya/WG/SRR11497836.vcf.gz. Error was: It doesn't exist.
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
slurm-14821231.out (END)
See forum topic details at forum guidelines page: https://gatk.broadinstitute.org/hc/en-us/articles/360053845952-Forum-Guidelines
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Hello,
I used GAYK/ 3 to combine multiple vcf files in the past, but it is no longer working. GenomeAnalysisTK -at 8 -T GenotypeGVCFs
Now, I tried to use this command to combine multiple vcf files.
gatk CombineGVCFs \
Please let me know if the CombineGVCFs do the same thing as the past version. Thanks.
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Hi Aziz,
Yes, CombineGVCFs in GATK4 is the same as CombineGVCFs in GATK3, with a few bug fixes. The error you are getting here looks like it could be from a typo in your command line or an issue with permissions:
A USER ERROR has occurred: Couldn't read file file:///scratch/brown/aebrahi/regia_ref2/carya/WG/SRR11497836.vcf.gz. Error was: It doesn't exist.
Once you resolve the issue with the file, CombineGVCFs should work just fine.
Best,
Genevieve
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