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joverlee521 avatar joverlee521 commented on July 19, 2024

Hi @limh25, thank you for reporting this issue.

You should be able to run the example build using the command:

nextstrain build .  --configfile profiles/ci/builds.yaml

I am updating the README to reflect this in #113.

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limh25 avatar limh25 commented on July 19, 2024

Hi @joverlee521,
Thank you for your help. Now it runs, but produces error and stops. Error message below.

[Tue Jul 25 06:42:49 2023]
Job 16: Parsing fasta into sequences and metadata
Reason: Missing output files: data/h3n2/na.fasta, data/h3n2/metadata_na.tsv; Input files updated by another job: data/h3n2/raw_na.fasta


        augur parse             --sequences data/h3n2/raw_na.fasta             --output-sequences data/h3n2/na.fasta             --output-metadata data/h3n2/metadata_na.tsv             --fields strain virus accession date date_submitted region country division location passage_category originating_lab submitting_lab age gender             --prettify-fields region country division location originating_lab submitting_lab 2>&1 | tee logs/parse_h3n2_na.txt
        
[Tue Jul 25 06:42:49 2023]
Error in rule concat_titers_for_build:
    jobid: 20
    input: example_data/cdc_h3n2_cell_fra_titers.tsv
    output: builds/ci_build/all_titers.tsv
    log: logs/concat_titers_for_build_ci_build.txt (check log file(s) for error details)
    conda-env: /app/limh25/seasonal-flu/.snakemake/conda/bda388b1eaf328dc458bca193b400f10_
    shell:
        
        tsv-append -H example_data/cdc_h3n2_cell_fra_titers.tsv > builds/ci_build/all_titers.tsv 2> logs/concat_titers_for_build_ci_build.txt
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job concat_titers_for_build since they might be corrupted:
builds/ci_build/all_titers.tsv
[Tue Jul 25 06:42:49 2023]
Error in rule build_reference_strains_table:
    jobid: 18
    input: config/h3n2/reference_strains.txt
    output: data/h3n2/reference_strains.tsv
    log: logs/build_reference_strains_table_h3n2.txt (check log file(s) for error details)
    conda-env: /app/limh25/seasonal-flu/.snakemake/conda/bda388b1eaf328dc458bca193b400f10_
    shell:
        
        csvtk add-header             --names strain             config/h3n2/reference_strains.txt             | csvtk uniq             | csvtk --out-tabs mutate2                 --name is_reference                 --expression "'True'" > data/h3n2/reference_strains.tsv
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job build_reference_strains_table since they might be corrupted:
data/h3n2/reference_strains.tsv
[Tue Jul 25 06:42:50 2023]
Finished job 10.
3 of 88 steps (3%) done
[Tue Jul 25 06:42:50 2023]
Finished job 16.
4 of 88 steps (5%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-07-25T064248.960339.snakemake.log

Should I turn off the titer part? If so, how am I supposed to run it without titer part?
Complete log file attached.

Thank you again.

2023-07-25T064248.960339.snakemake.log

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joverlee521 avatar joverlee521 commented on July 19, 2024

@limh25 Could you provide the logs for the first rule that failed (logs/concat_titers_for_build_ci_build.txt)? It should contain more details on the error.

Could you also provide the output of nextstrain version --verbose?

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limh25 avatar limh25 commented on July 19, 2024

@joverlee521 The logs/concat_titers_for_build_ci_build.txt shows only one line /usr/bin/bash: line 1: tsv-append: command not found/

(nextstrain) [limh25@machine1 seasonal-flu]$ nextstrain version --verbose
nextstrain.cli 6.1.0.post1

Python
  /home/limh25/anaconda3/envs/nextstrain/bin/python3.7
  3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:21) 
  [GCC 9.4.0]

Runners
  docker 
Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?
    unknown

  conda 
    nextstrain-base unknown

  singularity 
    docker://nextstrain/base (not present)

  ambient (default)
    augur 18.1.2
    auspice 2.39.0

  aws-batch 
    unknown

Thanks.

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limh25 avatar limh25 commented on July 19, 2024

@joverlee521 The example build works fine with nextstrain build . --configfile profiles/ci/builds.yaml. I have two machines where nextstrain is installed, and the one with newer installation works fine. I just have to update the older one.

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joverlee521 avatar joverlee521 commented on July 19, 2024

Glad to hear you were able to get it working!

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