Logging

Common Commands

Pipeline Status

sudo journalctl -u srsilo-update -n 1000

Errors

journalctl -p err --since today | grep srsilo

API Logs

# Container names follow pattern: <instance_name>-lapis / <instance_name>-silo
# COVID: wise-sarsCoV2-lapis, wise-sarsCoV2-silo
# RSV-A: wise-rsva-lapis, wise-rsva-silo
docker logs wise-sarsCoV2-lapis -f
docker logs wise-sarsCoV2-silo -f

# SILO file logs (per-virus)
tail -f /opt/srsilo/covid/logs/*.log
tail -f /opt/srsilo/rsva/logs/*.log

Timer

systemctl status srsilo-update.timer
systemctl list-timers srsilo-update.timer

Monitoring Services

journalctl -u prometheus -n 50
journalctl -u grafana-server -n 50

Kubernetes (Loculus)

kubectl logs <pod-name> -n <namespace> -f

Log Retention

Systemd Journal

System default (~1-2 months):

sudo journalctl --vacuum-time=2weeks  # Clean old logs

Docker Logs

Manual management at /opt/srsilo/<virus>/logs/:

# Archive old logs (per-virus)
cd /opt/srsilo/covid/logs
for log in *.log; do mv "$log" "$log.$(date +%Y%m%d)" && gzip "$log.$(date +%Y%m%d)"; done
find . -name "*.gz" -mtime +30 -delete