GenomicsDBImport

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Ali Basuony

• May 22, 2022 23:22
• Edited

I'm trying to run GenomicsDBImport step and got the following error.

REQUIRED for all errors and issues:
a) GATK version used:  gatk-4.2.2.0-gcc-8.4.1-ig3isjv
b) Exact command used: gatk

--java-options "-Xmx4g -Xms4g" GenomicsDBImport \
-V mnt/scratch/c1845371/ddRADfoxes202110_10/data/align_outredfoxB/read_group/ERR5417972RG.g.vcf.gz \
-V mnt/scratch/c1845371/ddRADfoxes202110_10/data/align_outredfoxB/read_group/SRR10769419RG.g.vcf.gz \
-V mnt/scratch/c1845371/ddRADfoxes202110_10/data/align_outredfoxB/read_group/SRR10769422RG.g.vcf.gz \
-R /mnt/scratch/c1845371/ddRADfoxes202110_10/V.vulpes_genome/GCF_003160815.1_VulVul2.2_genomic.fna \
       --genomicsdb-workspace-path ali_db
       -L  NW_020356435.1, NW_020356435.2

c) Entire program log:

A USER ERROR has occurred: Argument genomicsdb-workspace-path was missing: Argument 'genomicsdb-workspace-path' is required unless one of {[genomicsdb-update-workspace-path, output-interval-list-to-file]} are provided

***********************************************************************

A USER ERROR has occurred: Argument genomicsdb-workspace-path was missing: Argument 'genomicsdb-workspace-path' is required unless one of {[genomicsdb-update-workspace-path, output-interval-list-to-file]} are provided

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /trinity/shared/apps/spack/opt/spack/iago/gcc-8.4.1/gatk-4.2.2.0-ig3isjvlmuyjpezxojwdlkqr3arfgnen/bin/gatk-package-4.2.2.0-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 -Xmx4g -Xms4g -jar /trinity/shared/apps/spack/opt/spack/iago/gcc-8.4.1/gatk-4.2.2.0-ig3isjvlmuyjpezxojwdlkqr3arfgnen/bin/gatk-package-4.2.2.0-local.jar GenomicsDBImport -V mnt/scratch/c1845371/ddRADfoxes202110_10/data/align_outredfoxB/read_group/ERR5417972RG.g.vcf.gz -V mnt/scratch/c1845371/ddRADfoxes202110_10/data/align_outredfoxB/read_group/SRR10769419RG.g.vcf.gz -V mnt/scratch/c1845371/ddRADfoxes202110_10/data/align_outredfoxB/read_group/SRR10769422RG.g.vcf.gz -R /mnt/scratch/c1845371/ddRADfoxes202110_10/V.vulpes_genome/GCF_003160815.1_VulVul2.2_genomic.fna
/var/spool/slurmd/job52713/slurm_script: line 434: --genomicsdb-workspace-path: command not found

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I'm a new user of GATK and I think this is a simple problem, but I googled a bout it and didn't find a solution.

Thanks for help

0

• 

  Genevieve Brandt (she/her)

  • May 24, 2022 19:57

  Hi Ali Basuony,

  This looks like a small command line issue where there is a new line character after your reference file name. Your machine is reading the --genomicsdb-workspace-path argument as a new line.

  Thankfully it should be an easy fix once you find the issue!

  Best,

  Genevieve

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  Ali Basuony

  • May 27, 2022 14:46

  Hi Genevieve,

  Thanks so much for your reply.

  As you mentioned the probelm was some inactive lines between the command lines.

  It worked after removing the extra lines.

  Thanks

  Ali

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  Genevieve Brandt (she/her)

  • May 31, 2022 16:49

  Glad it's working! Thanks for posting your solution.

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