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Update yield metrics page after rerunning with checkpoint instead of savedmodel.
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docs/images/runtime_yield_v0.3.png

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docs/yield_metrics.md

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@@ -44,21 +44,21 @@ m64014_200920_132517 | HG002 | 2.2 | 24 kb
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<td>121.78%</td>
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<td>4.06 Gb</td>
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<td>167.33%</td>
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<td>301.46</td>
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<td>277.68</td>
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</tr>
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<tr>
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<td>v0.3</td>
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<td>m64008_201124_002822</td>
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<td>chem2.2_15kb</td>
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<td>2,689,147</td>
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<td>2,864,910</td>
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<td>2,864,908</td>
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<td>42.41 Gb</td>
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<td>106.09%</td>
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<td>30.41 Gb</td>
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<td>115.70%</td>
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<td>7.54 Gb</td>
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<td>191.51%</td>
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<td>739.09</td>
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<td>683.97</td>
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</tr>
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<tr>
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<td>v0.3</td>
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<td>149.24%</td>
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<td>1.60 Gb</td>
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<td>462.97%</td>
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<td>1,003.86</td>
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<td>925.01</td>
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</tr>
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</tbody>
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</table>
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e.g. 40% percent means that DeepConsensus increased yield of high quality
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reads in bases by 40% over CCS.
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These were run on GCP `n1-standard-32` machines with no GPU (in 500 shards,
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combined above), with `--batch_zmws=500 --batch_size=1024`. However, in our
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runtime tests we find that using `n1-standard-16` VMs with `--batch_zmws=100
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--batch_size=1024` has similar runtime with fewer CPUs and memory needed. For
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more information on compute setups, see the
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These were run on GCP `n1-standard-16` machines with no GPU (in 500 shards,
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combined above), with `--batch_zmws=100 --batch_size=1024`, which is generally
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what we recommend. For more information on compute setups, see the
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[runtime metrics page](runtime_metrics.md).
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## Runtime-yield tradeoffs with `--skip_windows_above`

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