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troubleshoot failed executions #11

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troubleshoot failed executions #11

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37 changes: 36 additions & 1 deletion notebooks/genotype_sg10k_dragen.md
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Original file line number Diff line number Diff line change
Expand Up @@ -62,18 +62,43 @@ docker run -it -v `pwd`:/data aldy:3.3 aldy genotype \
--profile illumina \
--gene CYP2D6 \
--reference hg38.fasta \
--output WHB3694-CYP2D6.aldy \
--output WHB3694.aldy \
WHB3694.cram

# manual execution completed successfully
# upload results to s3
cp WHB3694.aldy \
/data/SG10K-CYP2D6/s3/sg10k-cyp2d6-workspace/call_haplotypes/sg10k-dragen/outputs/WHB3694/aldy/
aws s3 sync \
/data/SG10K-CYP2D6/s3/sg10k-cyp2d6-workspace/call_haplotypes/sg10k-dragen/outputs/WHB3694/aldy/ \
s3://sg10k-cyp2d6-workspace/call_haplotypes/sg10k-dragen/outputs/WHB3694/aldy/
```

### aldy: WHB4149

Manually launch following instructions above

```bash
# manual execution completed with an error
# upload logs to s3 and notify authors
aws s3 sync /data/SG10K-CYP2D6/s3/sg10k-cyp2d6-workspace/call_haplotypes/sg10k-dragen/outputs/WHB4149/aldy/ \
s3://sg10k-cyp2d6-workspace/call_haplotypes/sg10k-dragen/outputs/WHB4149/aldy/
```

### aldy: WHB4689

Manually launch following instructions above

```bash
# manual execution completed successfully
# upload results to s3
cp WHB4689.aldy \
/data/SG10K-CYP2D6/s3/sg10k-cyp2d6-workspace/call_haplotypes/sg10k-dragen/outputs/WHB4689/aldy/
aws s3 sync \
/data/SG10K-CYP2D6/s3/sg10k-cyp2d6-workspace/call_haplotypes/sg10k-dragen/outputs/WHB4689/aldy/ \
s3://sg10k-cyp2d6-workspace/call_haplotypes/sg10k-dragen/outputs/WHB4689/aldy/
```

### Cyrius: WHB3978

```bash
Expand All @@ -95,6 +120,16 @@ docker run -it -v `pwd`:/data cyrius:1.1.1 star_caller.py \
--reference hg38.fasta \
--prefix WHB3978 \
--outDir ./

# manual execution completed succesfully
# upload results to s3
cp WHB3978.json \
/data/SG10K-CYP2D6/s3/sg10k-cyp2d6-workspace/call_haplotypes/sg10k-dragen/outputs/WHB3978/cyrius/
cp WHB3978.tsv \
/data/SG10K-CYP2D6/s3/sg10k-cyp2d6-workspace/call_haplotypes/sg10k-dragen/outputs/WHB3978/cyrius/
aws s3 sync \
/data/SG10K-CYP2D6/s3/sg10k-cyp2d6-workspace/call_haplotypes/sg10k-dragen/outputs/WHB3978/cyrius/ \
s3://sg10k-cyp2d6-workspace/call_haplotypes/sg10k-dragen/outputs/WHB3978/cyrius/
```


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