What's wrong with my GATK HaplotypeCaller step's codes?

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Han Li

• November 29, 2021 05:18

I use the Linux conda to install the GATK for uses and here's the conda list.

I use the code as this .  I'm sure the path for these data is correct, but the Linux always return an error like ".fasta is not a recognized option" or  like the figure i Shown here. SO , I am wondering what's wrong and how i can do to debug the code? Thx

/home/anaconda3/envs/velocyto/bin/gatk --java-options "-Xmx4g" HaplotypeCaller \
-R /media/workspace/refdata-cellranger-GRCh38-3.0.0/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta \
-I /media/workspace/A3_90/outs/possorted_genome_bam.bam \
-D /media/workspace/refdata-cellranger-GRCh38-3.0.0/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf \
-ERC GVCF \
-O /media/A3_90.vcf

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  Pamela Bretscher

  • November 29, 2021 14:29
  • Edited

  Hi Han Li,

  This particular error tends to occur when there is some sort of typo in your command line which impacts how the tool reads the command. I am trying to look through your command to find a possible typo, could you go through and check for any extra/missing spaces or incorrect characters? Here are some similar posts regarding the same problem:

  https://gatk.broadinstitute.org/hc/en-us/community/posts/360076948391--No-positional-argument-is-defined-Error-in-HaplotypeCaller

  https://gatk.broadinstitute.org/hc/en-us/community/posts/360077380972-ApplyBQSR-no-positional-argument-is-defined-for-this-tool

  Kind regards,

  Pamela

   

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