6 assemblies with missing files

[anna-parker]

details in https://loculus.slack.com/archives/C0757PTR607/p1772183734471099

Assembly submission was interrupted due to a rollout (?) leading to some files being missing:

webin-cli/genome/PP_004JXQF.1/tmpusw0yr2j.gz | Missing file | 836017010ffb33b25e528a108333f6c1 | 69 | 16-FEB-26 | REDACTED
webin-cli/genome/PP_004JVG0.1/tmp1l8kl4zg.gz | Missing file | 4e8ca31d0d6c93a7ae20a87d96f2591a | 69 | 16-FEB-26 | REDACTED
webin-cli/genome/PP_004JVJV.1/tmpm9tgzy02.gz | Missing file | 7db7fc54a3e2f7de628fbaeeb1ef6567 | 69 | 16-FEB-26 | REDACTED
webin-cli/genome/PP_004JWF1.1/tmpsd3_ecw6.gz | Missing file | 5edd68037f8d74260eccae9bc1f7ae00 | 69 | 16-FEB-26 | REDACTED
webin-cli/genome/PP_004JWGZ.1/tmp6a09gfd9.gz | Missing file | 1ca5e87ce20a0af71e60e98c5394922e | 69 | 16-FEB-26 | REDACTED
webin-cli/genome/PP_004JVHX.1/tmpgfjjldze.gz | Missing file | 3774138061c926d0253609736bbe6936 | 69 | 16-FEB-26 | REDACTED

Sadly I cannot resubmit the files with the same alias as then ENA errors my submission saying it already exists. The only way to do fix this IMO is to "revise" the assemblies, i.e. resubmit them with a different alias.

[anna-parker]

Steps:

• Get the PPX ENA deposition submission config from argocd
• download the json file that was submitted
• get the centerName, biosample and bioproject accessions of each submission: all have the same PRJEB108342 and center name Stellenbosch University
• store ena broker creds as an env variable
• for each submission generate the assembly using the dry run script, add correct bioproject, biosample and new alias, submit assembly -> store new ERZ
• add new ERZ to db

[anna-parker]

They were submitted here: #228

jq 'with_entries(select(.key | IN(
  "PP_004JXQF.1",
  "PP_004JVG0.1",
  "PP_004JVJV.1",
  "PP_004JWF1.1",
  "PP_004JWGZ.1",
  "PP_004JVHX.1"
)))' input.json > filtered.json

put each into its own json file for dry run script:

jq -r 'keys[]' filtered.json | while read key; do
  jq --arg k "$key" '{($k): .[$k]}' filtered.json > "$key.json"
done

set -euo pipefail

declare -A biosample_by_acc=(
  ["PP_004JXQF.1"]="SAMEA121577075"
  ["PP_004JVG0.1"]="SAMEA121577077"
  ["PP_004JVJV.1"]="SAMEA121577079"
  ["PP_004JWF1.1"]="SAMEA121577080"
  ["PP_004JWGZ.1"]="SAMEA121577081"
  ["PP_004JVHX.1"]="SAMEA121577078"
)

accessions=(
  "PP_004JXQF.1"
  "PP_004JVG0.1"
  "PP_004JVJV.1"
  "PP_004JWF1.1"
  "PP_004JWGZ.1"
  "PP_004JVHX.1"
)

for acc in "${accessions[@]}"; do
  biosample="${biosample_by_acc[$acc]}"

  echo "=== Processing $acc (biosample: $biosample) ==="

  python scripts/deposition_dry_run.py \
    --log-level=DEBUG \
    --data-to-submit="${acc}.json" \
    --mode=assembly \
    --center-name="Stellenbosch University" \
    --bioproject="PRJEB108342" \
    --biosample="$biosample" \
    --config-file=config/config.yaml

  ena-webin-cli \
    -username "$ena_submission_username" \
    -password "$ena_submission_password" \
    -context genome \
    -manifest assembly/manifest.tsv \
    -submit -test \
    -centername 'Stellenbosch University'

  rm -rf assembly
done