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Projects 12 active · 3,214 samples · 60.8 TBsynthetic Science workspace
| ID | Project | Lead | Samples | Pipeline | Data | Stage | Updated |
|---|---|---|---|---|---|---|---|
| PRJ-0417 | Bladder ctDNA urine panel | Dr I. Hart | 384 | sarek 3.5.1 | 4.1 TB | Calling | 11:42 |
| PRJ-0412 | FGFR3 variant atlas | Dr K. Mensah | 1,212 | sarek 3.5.1 | 11.8 TB | Annotating | 10:58 |
| PRJ-0409 | Evo 2 40B effect benchmark | Dr R. Calloway | 52,000 | evo2-score 1.4.0 | 0.6 TB | Scoring | 10:31 |
| PRJ-0405 | MedGemma 27B report QA | Dr S. Pillai | 2,400 | medgemma-eval 0.6.2 | 0.2 TB | Evaluating | 09:47 |
| PRJ-0398 | Single-cell bladder TME | Dr E. Kowalczyk | 48 | scrnaseq 2.7.1 | 6.3 TB | QC warn | 09:12 |
| PRJ-0391 | Wearable HRV cohort | Dr T. Ashdown | 1,050 | edge-signals 0.9.3 | 0.9 TB | Features | 08:55 |
| PRJ-0388 | Methylation cfDNA | Dr L. Okafor | 220 | methylseq 2.7.1 | 3.4 TB | Aligning | 08:20 |
| PRJ-0384 | RNA-seq NMIBC recurrence | Dr H. Reid | 312 | rnaseq 3.17.0 | 5.2 TB | Done | Fri |
| PRJ-0379 | Pathology WSI tiling | Dr P. Nair | 1,840 | wsi-tiler 2.1.0 | 21.7 TB | Tiling | Fri |
| PRJ-0372 | Colonoscopy polyp model | Dr O. Price | 9,600 | yolo-med 1.2.0 | 2.8 TB | Training | Thu |
| PRJ-0366 | Retinal DR grading audit | Dr A. Rahman | 14,200 | desp-grader 3.0.1 | 1.6 TB | Done | Wed |
| PRJ-0361 | Long-read SV pilot | Dr F. Gallagher | 24 | nanoseq 3.1.0 | 2.2 TB | Paused | 2 Oct |
Recent runs ledger every run signed · Nextflow 24.10.2 · reproducible by commit16 shown · 412 in Oct
| Run | Project | Pipeline | Started | Took | Compute | GPU h | Cost | Exit |
|---|---|---|---|---|---|---|---|---|
| RUN-24117 | PRJ-0417 | sarek 3.5.1 | 10:42 | 1h 12m | Civo A100 | 1.2 | £4.14 | Running |
| RUN-24116 | PRJ-0409 | evo2-score 1.4.0 | 09:58 | 41m | Civo A100 | 0.7 | £2.36 | Exit 0 |
| RUN-24115 | PRJ-0405 | medgemma-eval 0.6.2 | 09:10 | 38m | JudeBox L4 | 1.3 | £0.94 | Exit 0 |
| RUN-24114 | PRJ-0398 | scrnaseq 2.7.1 | 08:31 | 52m | Civo CPU | 0.0 | £1.12 | Exit 1 |
| RUN-24113 | PRJ-0412 | sarek 3.5.1 | 07:05 | 3h 37m | Civo A100 | 3.6 | £12.42 | Exit 0 |
| RUN-24112 | PRJ-0391 | edge-signals 0.9.3 | 06:40 | 14m | Mac M4 Max | 0.2 | £0.00 | Exit 0 |
| RUN-24111 | PRJ-0388 | methylseq 2.7.1 | 05:12 | 6h 02m | Civo CPU | 0.0 | £6.88 | Exit 0 |
| RUN-24110 | PRJ-0409 | evo2-score 1.4.0 | 03:48 | 44m | Civo A100 | 0.7 | £2.53 | Exit 0 |
| RUN-24109 | PRJ-0379 | wsi-tiler 2.1.0 | 01:20 | 2h 11m | JudeBox L4 | 4.4 | £3.17 | Exit 0 |
| RUN-24108 | PRJ-0372 | yolo-med 1.2.0 | Sun 22:02 | 5h 18m | Civo A100 | 5.3 | £18.29 | Exit 0 |
| RUN-24107 | PRJ-0405 | medgemma-eval 0.6.2 | Sun 19:41 | 35m | JudeBox L4 | 1.2 | £0.86 | Exit 0 |
| RUN-24106 | PRJ-0412 | sarek 3.5.1 | Sun 16:15 | 3h 51m | Civo A100 | 3.9 | £13.32 | Exit 0 |
| RUN-24105 | PRJ-0361 | nanoseq 3.1.0 | Sun 14:02 | 1h 06m | Civo CPU | 0.0 | £1.48 | Exit 137 |
| RUN-24104 | PRJ-0398 | scrnaseq 2.7.1 | Sun 11:30 | 4h 58m | Civo CPU | 0.0 | £5.66 | Exit 0 |
| RUN-24103 | PRJ-0417 | sarek 3.5.1 | Sun 09:17 | 3h 44m | Civo A100 | 3.7 | £12.77 | Exit 0 |
| RUN-24102 | PRJ-0384 | rnaseq 3.17.0 | Sun 06:58 | 1h 58m | Civo CPU | 0.0 | £2.21 | Exit 0 |
Pipelines 9 pinned by version and container digestNextflow 24.10.2
| Pipeline | Version | Engine | Runs 30d | Success | Median | Lock |
|---|---|---|---|---|---|---|
| nf-core/sarek | 3.5.1 | Nextflow | 41 | 97.6% | 3h 44m | Pinned |
| nf-core/rnaseq | 3.17.0 | Nextflow | 28 | 100% | 1h 58m | Pinned |
| nf-core/scrnaseq | 2.7.1 | Nextflow | 9 | 88.9% | 5h 10m | Review |
| nf-core/methylseq | 2.7.1 | Nextflow | 12 | 91.7% | 6h 02m | Pinned |
| nf-core/nanoseq | 3.1.0 | Nextflow | 3 | 66.7% | 1h 20m | Review |
| deepvariant | 1.8.0 | Docker · GPU | 37 | 100% | 48m | Pinned |
| evo2-score | 1.4.0 | PyTorch · GPU | 64 | 98.4% | 41m | Pinned |
| medgemma-eval | 0.6.2 | vLLM · GPU | 22 | 95.5% | 36m | Pinned |
| wsi-tiler | 2.1.0 | Python · GPU | 18 | 100% | 2h 11m | Pinned |
Civo GPU compute and cost October · measured, not estimated1 A100 at a time
GPU hours, Oct1,284 h▲ 18% vs Sep
Spend, Oct£3,51235% of £10,000
Running now2 GPUsA100 + L4
Queued3 jobswaiting on A100
| Node | GPU | Util | Memory | Job |
|---|---|---|---|---|
| civo-a100-lon1-01 | A100 80GB | 92% | 71 / 80 GB | RUN-24117 |
| civo-a100-lon1-02 | A100 80GB | 0% | Quota: 1 A100 | 3 queued |
| civo-h100-* | H100 80GB | 0% | Region out | n/a |
| judebox-l4-mcr-02 | L4 24GB | 64% | 15 / 24 GB | RUN-24118 |
| judebox-l4-mcr-01 | L4 24GB | 81% | 19 / 24 GB | RUN-24109 |
| jetson-orin-edge-07 | Orin 64GB | 23% | 11 / 64 GB | Fundus triage |
| mac-m4max-aa | 40-core GPU | 18% | 9 / 64 GB | Jude inference |
PRJ-0417 Bladder ctDNA urine panelCalling
LeadDr I. HartSponsorCRUK · C61473/A29012EthicsREC 24/NW/0187 · IRAS 331842Samples384 urine cfDNA · 96 bloodReferenceGRCh38 · GENCODE 46 · VEP 112Data4.1 TB · Civo object store LON1Pipelinenf-core/sarek 3.5.1 · pinnedSpend to date£1,284.60 of £4,000
Stages212 of 384 called
| FASTQ QC | 384/384 | |
| Align BWA-MEM2 | 384/384 | |
| Mark duplicates | 384/384 | |
| Call Mutect2 | 212/384 | |
| Annotate VEP 112 | 0/384 |
Timeline12 Oct
| 07:02 Batch 3 FASTQ landed, 96 samples |
| 08:40 QC passed, 2 flagged low yield |
| 10:42 RUN-24117 started on A100 |
| 11:30 Jude: 172 samples still to call |
Next decision
Run172 samples · Mutect2 GPUEst.6.2 GPU h · £21.39PlacementCivo A100 after 13:40
Approve on A100Use JudeBox L4
Budget owner approves over £50 · receipt to audit chain
Flagged samples3 of 384
| Sample | Issue | Reads |
|---|---|---|
| BLD-0417-207 | Low yield | 3.1 M |
| BLD-0417-233 | Low yield | 2.7 M |
| BLD-0417-288 | Swap check | 18.4 M |
Tell Jude what you intend to do
JudeAI · Qwen 27B on Civo