Error in Rule Refine when run ncov

Help and Getting Started
1

Hello, please help me, i have been trying run the ncov region indonesia, when run with command “nextstrain build . --configfile build.yaml --use-conda -p”

contents of the file build.yaml

inputs:

  - name: jawa_barat
    metadata: data/indonesia/jawabarat/jawabarat_metadata.tsv
    sequences: data/indonesia/jawabarat/jawabarat_sequences.fasta

  - name: asia
    metadata: data/asia/asia_metadata.tsv
    sequences: data/asia/asia_sequences.fasta

builds:
  asia_indonesia_jawabarat:
    subsampling_scheme: division
    region: Asia
    country: Indonesia
    division: Jawa Barat

  asia_indonesia:
    subsampling_scheme: country
    region: Asia
    country: Indonesia

  asia:
    subsampling_scheme: region
    region: Asia

  global:
    subsampling_scheme: region_global
    region: global

subsampling:

  custom-county:
    focal:
      group_by: "year month"
      seq_per_group: 300
      query: --query "(country == '{country}') & (division == '{division}')
    related:
      group_by: "country year month"
      seq_per_group: 20
      exclude: "--exclude-where 'division={division}'"
      priorities:
        type: "proximity"
        focus: "focal"
    contextual:
      group_by: "country year month"
      seq_per_group: 10
      exclude: "--exclude-where 'division={division}'"

files:
  auspice_config: "my_profiles/indonesia/my_auspice_config.json"
  description: "my_profiles/indonesia/my_description.md"

i get error :

/usr/bin/bash: line 1: 224417 Killed                  augur refine --tree results/asia_indonesia_jawabarat/tree_raw.nwk --alignment results/asia_indonesia_jawabarat/masked.fasta --metadata results/asia_indonesia_jawabarat/metadata_adjusted.tsv.xz --output-tree results/asia_indonesia_jawabarat/tree.nwk --output-node-data results/asia_indonesia_jawabarat/branch_lengths.json --root Wuhan/Hu-1/2019 --timetree --clock-rate 0.0008 --clock-std-dev 0.0004 --coalescent opt --date-inference marginal --divergence-unit mutations --date-confidence --no-covariance --clock-filter-iqd 4 2>&1
     224418 Done                    | tee logs/refine_asia_indonesia_jawabarat.txt
[Fri Dec 24 07:43:12 2021]
Error in rule refine:
    jobid: 5
    output: results/asia_indonesia_jawabarat/tree.nwk, results/asia_indonesia_jawabarat/branch_lengths.json
    log: logs/refine_asia_indonesia_jawabarat.txt (check log file(s) for error message)
    conda-env: /home/nextstrain/ncov/.snakemake/conda/5e42b16fb0f0152881befe875b00574f
    shell:

        augur refine             --tree results/asia_indonesia_jawabarat/tree_raw.nwk             --alignment results/asia_indonesia_jawabarat/masked.fasta             --metadata results/asia_indonesia_jawabarat/metadata_adjusted.tsv.xz             --output-tree results/asia_indonesia_jawabarat/tree.nwk             --output-node-data results/asia_indonesia_jawabarat/branch_lengths.json             --root Wuhan/Hu-1/2019             --timetree                          --clock-rate 0.0008             --clock-std-dev 0.0004             --coalescent opt             --date-inference marginal             --divergence-unit mutations             --date-confidence             --no-covariance             --clock-filter-iqd 4 2>&1 | tee logs/refine_asia_indonesia_jawabarat.txt

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
version augur : 13.1.0

Thanks
Rian

2

Hi Rian – the augur refine step is being killed, but it’s unclear to me why from the details you’ve provided. Could you post the output of logs/refine_asia_indonesia_jawabarat.txt? My guess is running out of memory but I can’t be sure.

It would help to know what runtime nextstrain build is using. Could you also post the output of running nextstrain check-setup to help determine this?

3

thank you very much for your answer, I already got the solution by following the instructions Prepare GISAID data for Augur from Preparing your data — SARS-CoV-2 Workflow documentation (nextstrain.org) after following these instructions I can build, the build process becomes faster.