Hello, I am using docker command first time, so not much aware of it, i am trying

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docker: invalid reference format. about deepvariant HOT 6 CLOSED

Jyoti-Mridha commented on September 25, 2024

docker: invalid reference format.

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Jyoti-Mridha commented on September 25, 2024 1

Hi, Thanks a lot for your great help, Now I am able to run the command and get my results.👍 docker run -v /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3:/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3 -v /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result:/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result google/deepvariant:1.6.1 /opt/deepvariant/bin/run_deepvariant --reads /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3/MITO60_sorted.bam --ref /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3/hg38_chrM.fa --report_title MITO60_Stats --sample_name MITO60 --output_vcf /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result/deepvariant_MITO60.vcf.gz --model_type ONT_R104

…

On Wed, Jun 12, 2024 at 1:02 PM JYOTI MRIDHA ***@***.***> wrote: Hi, Thanks a lot for your immediate response, i have followed the above instructions given by you, now the docker command is running fine, but I have come across a new error. *[E::hts_open_format] Failed to open file "/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result" : Is a directory* *ValueError: UNKNOWN: Could not open variants_path: /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result* here i have used the same path for docker run (-v /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result:/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result) and also same path for run_deepvariant (--output_vcf /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result ) , Here i am not able to rectify what minor error in my command, i am following the same pattern mentioned in the link shared, i might be missing out something minute. Here is my command which is used. sudo docker run -v /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3:/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3 -v /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result:/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result google/deepvariant:1.6.1 /opt/deepvariant/bin/run_deepvariant --reads /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3/MITO60_sorted.bam --ref /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3/hg38_chrM.fa --report_title MITO60_Stats --sample_name MITO60 --output_vcf /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result --model_type ONT_R104 On Wed, Jun 12, 2024 at 12:03 PM Pi-Chuan Chang ***@***.***> wrote: > And, just in case the documentation isn't clear: > > This part: > > sudo docker run \ > -v "${INPUT_DIR}":"/input" \ > -v "${OUTPUT_DIR}":"/output" \ > google/deepvariant:"${BIN_VERSION}" \ > ... > > The variable BIN_VERSION was specified in earlier in the steps: > > BIN_VERSION="1.6.1" > > So, in Unix command it's equivalent to: > > google/deepvariant:"1.6.1" \ > > — > Reply to this email directly, view it on GitHub > <#829 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/BDQL2ZE35INJI4WP7BHRNK3ZG7TVPAVCNFSM6AAAAABJFTFWYKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRSGIYTANZWGM> > . > You are receiving this because you were mentioned.Message ID: > ***@***.***> >

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pichuan commented on September 25, 2024

Can you check your FASTA file has corresponding index files?

What do you see what you run:

ls /media/manish/Data/Jyoti_Mridha_AIC/My_S/Nanopore_Mito/Mito_Genome_hg38/zip_ref_docker/hg38_chrM.fa.gz*

And, just as a check, can you confirm whether you were able to run https://github.com/google/deepvariant/blob/r1.6.1/docs/deepvariant-quick-start.md ?

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Jyoti-Mridha commented on September 25, 2024

Yes i do have a faidx index file too, actually i am doing it with mitochondrial genome for hg38 version. Again i modified the command kept both input sorted bam and fasta file along with faidx index in the same directory, By following the given format https://github.com/google/deepvariant/blob/r1.6.1/docs/deepvariant-ont-r104-simplex-case-study.md BIN_VERSION="1.6.1" sudo docker run \ -v "${INPUT_DIR}":"${INPUT_DIR}" \ -v "${OUTPUT_DIR}":"${OUTPUT_DIR}" \ google/deepvariant:"${BIN_VERSION}" \ /opt/deepvariant/bin/run_deepvariant \ --model_type ONT_R104 \ --ref "${INPUT_DIR}/${REF}" \ --reads "${INPUT_DIR}/${BAM}" \ --output_vcf "${OUTPUT_DIR}/${OUTPUT_VCF}" \ --output_gvcf "${OUTPUT_DIR}/${OUTPUT_GVCF}" \ --num_shards "${THREADS}" \ --regions "${REGION}" \ --intermediate_results_dir "${OUTPUT_DIR}/${INTERMEDIATE_DIRECTORY}" => Here is my recent command used for docker run. It would be great help if I am able to resolve this issue. Thank you in advance. sudo docker run -v */media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3:/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3* -v /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result:/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result google/deepvariant:{BIN_VERSION="1.6.1"} python /media/manish/Data/Jyoti_Mridha_AIC/Program/deepvariant-1.6.1/scripts/run_deepvariant.py *--reads /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3/MITO60_sorted.bam --ref /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3/hg38_chrM.fa *--report_title MITO60_Stats --sample_name MITO60 --output_vcf /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result/ --model_type ONT_R104

…

On Wed, Jun 12, 2024 at 11:20 AM Pi-Chuan Chang ***@***.***> wrote: Can you check your FASTA file has corresponding index files? What do you see what you run: ls /media/manish/Data/Jyoti_Mridha_AIC/My_S/Nanopore_Mito/Mito_Genome_hg38/zip_ref_docker/hg38_chrM.fa.gz* And, just as a check, can you confirm whether you were able to run https://github.com/google/deepvariant/blob/r1.6.1/docs/deepvariant-quick-start.md ? — Reply to this email directly, view it on GitHub <#829 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BDQL2ZEKDU5WYOAUIP24CJLZG7OSVAVCNFSM6AAAAABJFTFWYKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRSGE2TONJUHE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

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pichuan commented on September 25, 2024

Hi @Jyoti-Mridha ,

I looked at your error again more closely, and I realize that docker: invalid reference format. is not referring to the FASTA file.
It is something to do with your command, which doesn't have the correct format of how you would use Docker.

For example, if I run:

sudo docker run google/deepvariant:1.6.1 /opt/deepvariant/bin/run_deepvariant --helpshort

which shows me the flags.

But if I run something similar to your command:

sudo docker run google/deepvariant:{BIN_VERSION="1.6.1"} /opt/deepvariant/bin/run_deepvariant --helpshort

It gave me this error:

docker: invalid reference format.
See 'docker run --help'.

I think there might be other formatting errors in your command.

My suggestion: Can you make sure you follow our Quick Start step-by-step first?
And, once that succeed, please make sure you use a command similar to https://github.com/google/deepvariant/blob/r1.6.1/docs/deepvariant-quick-start.md#run-deepvariant-with-one-command

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pichuan commented on September 25, 2024

And, just in case the documentation isn't clear:

This part:

sudo docker run \
  -v "${INPUT_DIR}":"/input" \
  -v "${OUTPUT_DIR}":"/output" \
  google/deepvariant:"${BIN_VERSION}" \
  ...

The variable BIN_VERSION was specified in earlier in the steps:

BIN_VERSION="1.6.1"

So, in Unix command it's equivalent to:

  google/deepvariant:"1.6.1" \

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Jyoti-Mridha commented on September 25, 2024

Hi, Thanks a lot for your immediate response, i have followed the above instructions given by you, now the docker command is running fine, but I have come across a new error. *[E::hts_open_format] Failed to open file "/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result" : Is a directory* *ValueError: UNKNOWN: Could not open variants_path: /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result* here i have used the same path for docker run (-v /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result:/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result) and also same path for run_deepvariant (--output_vcf /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result ) , Here i am not able to rectify what minor error in my command, i am following the same pattern mentioned in the link shared, i might be missing out something minute. Here is my command which is used. sudo docker run -v /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3:/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3 -v /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result:/media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result google/deepvariant:1.6.1 /opt/deepvariant/bin/run_deepvariant --reads /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3/MITO60_sorted.bam --ref /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/Batch1_3runs/1_minimap2_freebayes_Final/Direct_minimap/Bam/run3/hg38_chrM.fa --report_title MITO60_Stats --sample_name MITO60 --output_vcf /media/manish/Data/Jyoti_Mridha_AIC/Nanopore_Sequencing/Jyoti_mito_Analysis_GATK/1_FINAL_NANOPORE/deepvariants_Trial/deepvariant_result --model_type ONT_R104

…

On Wed, Jun 12, 2024 at 12:03 PM Pi-Chuan Chang ***@***.***> wrote: And, just in case the documentation isn't clear: This part: sudo docker run \ -v "${INPUT_DIR}":"/input" \ -v "${OUTPUT_DIR}":"/output" \ google/deepvariant:"${BIN_VERSION}" \ ... The variable BIN_VERSION was specified in earlier in the steps: BIN_VERSION="1.6.1" So, in Unix command it's equivalent to: google/deepvariant:"1.6.1" \ — Reply to this email directly, view it on GitHub <#829 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BDQL2ZE35INJI4WP7BHRNK3ZG7TVPAVCNFSM6AAAAABJFTFWYKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRSGIYTANZWGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

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docker: invalid reference format. about deepvariant HOT 6 CLOSED

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