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rimo
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figured out a solution!
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rimo
rimo
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I'm trying to use the HaplotypeCaller from the GATK toolkit but I keep getting an error. I pulled GATK through Docker and am using this command:

docker run -v /Users/rimo/ -it broadinstitute/gatk:latest gatk HaplotypeCaller -R /Users/rimo/reference.fasta -I /Users/rimo/sample1.bam -O /Users/rimo/sample1.g.vcf.gz -ERC GVCF

/Users/rimo is my home directory it's where the files are currently located on my computer and it's where I want GATK to look for files to use in the command.

but then I get this error:

A USER ERROR has occurred: The specified fasta file (file:///Users/rimo/reference.fasta) does not exist.

I don't fully understand how Docker commands work but I found a similar problem listed with this issue. I tried to use their solution but it's still giving me the same error as listed above.

I'm trying to use the HaplotypeCaller from the GATK toolkit but I keep getting an error. I pulled GATK through Docker and am using this command:

docker run -v /Users/rimo/ -it broadinstitute/gatk:latest gatk HaplotypeCaller -R /Users/rimo/reference.fasta -I /Users/rimo/sample1.bam -O /Users/rimo/sample1.g.vcf.gz -ERC GVCF

/Users/rimo is my home directory it's where the files are currently located on my computer and it's where I want GATK to look for files to use in the command.

but then I get this error:

A USER ERROR has occurred: The specified fasta file (file:///Users/rimo/reference.fasta) does not exist.

I don't fully understand how Docker commands work but I found a similar problem listed with this issue. I tried to use their solution but it's still giving me the same error as listed above.

I'm trying to use the HaplotypeCaller from the GATK toolkit but I keep getting an error. I pulled GATK through Docker and am using this command:

docker run -v /Users/rimo/ -it broadinstitute/gatk:latest gatk HaplotypeCaller -R /Users/rimo/reference.fasta -I /Users/rimo/sample1.bam -O /Users/rimo/sample1.g.vcf.gz -ERC GVCF

/Users/rimo is my home directory it's where the files are currently located on my computer and it's where I want GATK to look for files to use in the command.

but then I get this error:

A USER ERROR has occurred: The specified fasta file (file:///Users/rimo/reference.fasta) does not exist.

I don't fully understand how Docker commands work but I found a similar problem listed with this issue. I tried to use their solution but it's still giving me the same error as listed above.

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rimo
rimo
  • 1.1k
  • 3
  • 18

How to run a GATK Docker Image with local files?

I'm trying to use the HaplotypeCaller from the GATK toolkit but I keep getting an error. I pulled GATK through Docker and am using this command:

docker run -v /Users/rimo/ -it broadinstitute/gatk:latest gatk HaplotypeCaller -R /Users/rimo/reference.fasta -I /Users/rimo/sample1.bam -O /Users/rimo/sample1.g.vcf.gz -ERC GVCF

/Users/rimo is my home directory it's where the files are currently located on my computer and it's where I want GATK to look for files to use in the command.

but then I get this error:

A USER ERROR has occurred: The specified fasta file (file:///Users/rimo/reference.fasta) does not exist.

I don't fully understand how Docker commands work but I found a similar problem listed with this issue. I tried to use their solution but it's still giving me the same error as listed above.