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perf(silo-prepro): speed up by using more efficient jq command (#3396)
It truned out that `jq -c '.'` was rate limiting and causing significant extra processing time. New command has been tested for correctness and performance, still validates. see https://loculus.slack.com/archives/C05G172HL6L/p1733500150097089?thread_ts=1733478069.696049&cid=C05G172HL6L
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