Sequencing Analysis State - 2026-05-18
CloudFront report URLs below use the shared LSMC QC Basic Auth credentials. Username: lsmc-qc-curious. The password was shared separately and is not stored in this document.
Sequencing Run QC
Run QC Reports
| Scope | Status | URL |
|---|---|---|
| Illumina run QC, all runs | In development | https://dlqovrcm5y71h.cloudfront.net/analysis_results/jem-scratch/run_qc_illumina_all/illumina_runs.multiqc.html |
| ONT run QC, all runs | In development | https://dlqovrcm5y71h.cloudfront.net/analysis_results/ubuntu/run_qc_ont_all/ont_runs.multiqc.html |
| Ultima run QC, all runs | No public tool yet | Pending |
Run State Summary
| Platform | <transferring> |
<in progress> |
<demuxed> |
<Aligned> |
<QC complete> |
<Exception> |
Total |
|---|---|---|---|---|---|---|---|
| Ultima | 0 | 0 | 5 | 3 | 1 | 1 | 10 |
| Illumina | 0 | 1 | 1 | 1 | 0 | 2 | 5 |
| ONT | 0 | 0 | 0 | 0 | 3 | 0 | 3 |
Illumina Source Run QC
| Run | Raw sequence data S3 URI | Demux summary |
|---|---|---|
LH01106_06MAR2026_PhiX_140pm_A |
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260306_LH01106_0001_A23KV7KLT4/ |
Demux stats are present and show 100.0000% called reads with 0 undetermined reads. No BCLConvert quality metrics or fastq-list report artifacts were found in the checked S3 paths. |
LH01106_06MAR2026_PhiX_140pm_B |
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260306_LH01106_0002_B23KV37LT4/ |
Demux stats are present and show 100.0000% called reads with 0 undetermined reads. No BCLConvert quality metrics or fastq-list report artifacts were found in the checked S3 paths. |
20260324_ILMN_training_instr_val |
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260324_LH01106_0003_B23KV2VLT4/ |
A SampleSheet and CopyComplete.txt are present, but no demux stats, BCLConvert quality metrics, or fastq-list artifacts were found in the checked S3 paths. |
20260407_ILMN_training_instr_val_2 |
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260407_LH01106_0004_A23K5LJLT4/ |
A SampleSheet and CopyComplete.txt are present, but no demux stats, BCLConvert quality metrics, or fastq-list artifacts were found in the checked S3 paths. |
20260507_23andMe_run-1 |
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260507_LH01106_0005_A23K3JVLT4/ |
BCLConvert report artifacts exist for 96 samples across 8 lanes with 93.3175% Q30. No Demultiplex_Stats.csv or unknown-barcode demux stats were found in the checked S3 paths. |
20260512_ILMN_Altair_Run_1 |
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260512_LH01106_0006_A23K3H2LT4/ |
Demux completed and is usable: 85.6783% called reads, 14.3217% undetermined reads, all 41 SampleSheet samples nonzero, and 92.9441% Q30. The largest top-unknown barcode entry is small relative to total reads. |
20260512_ILMN_Altair_Run_2 |
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260512_LH01106_0007_B23K5JKLT4/ |
Demux artifacts are present, but demux effectively failed: only 8 called reads total, with 33,436,817,267 reads undetermined, despite 93.3194% Q30. The top 8,000 unknown barcode pairs did not match this run's SampleSheet expected pairs or individual index sequences in the prior check. |
20260514_23andMe_run-2 |
s3://lsmc-ssf-sequencing-data/raw/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0008_A23TVNWLT4/ |
Transfer marker OOW.done is present in the raw S3 prefix, but no demux stats, BCLConvert quality metrics, or fastq-list artifacts were found there. This appears to be raw source data only in the checked prefix. |
20260514_ILMN_Altair_Run_3 |
s3://lsmc-ssf-sequencing-data/raw/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0009_B23TVLGLT4/ |
Demux artifacts are present and look usable: 87.0563% called reads, 12.9437% undetermined reads, all 41 SampleSheet samples nonzero, and 94.3353% Q30. Caveat: the raw S3 prefix currently has OOW.err, so the S3 transfer state is not clean even though demux CSVs are present. |
Run Analysis
Ultima
504632-20260326_2146 <demuxed>
- Run Name:
504632-20260326_2146<demuxed> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN504632/2026/504632-20260326_2146/ - Results S3: pending; no DayOA analysis result directory was found in the checked analysis prefixes.
- Alignstats data: pending.
- MultiQC report: pending.
505069-20260326_1848 <demuxed>
- Run Name:
505069-20260326_1848<demuxed> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN505069/2026/505069-20260326_1848/ - Results S3: pending; no DayOA analysis result directory was found in the checked analysis prefixes.
- Alignstats data: pending.
- MultiQC report: pending.
504970-20260331_1722 <Aligned>
- Run Name:
504970-20260331_1722<Aligned> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN504970/2026/504970-20260331_1722/ - Results S3:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260421T065118Z/analysis_results/ubuntu/prod-alignstats-504970-20260331-1722-20260425T091209Z/daylily-omics-analysis/results/day/hg38_broad/ - Alignstats data:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260421T065118Z/analysis_results/ubuntu/prod-alignstats-504970-20260331-1722-20260425T091209Z/daylily-omics-analysis/results/day/hg38_broad/other_reports/alignstats_gs_mqc.tsv - MultiQC report: pending; no
DAY_final_multiqc.htmlwas found in the checked results report directory.
505064-20260331_2020 <Aligned>
- Run Name:
505064-20260331_2020<Aligned> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN505064/2026/505064-20260331_2020/ - Results S3:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260421T065118Z/analysis_results/ubuntu/prod-alignstats-505064-20260331-2020-20260425T090724Z/daylily-omics-analysis/results/day/hg38_broad/ - Alignstats data:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260421T065118Z/analysis_results/ubuntu/prod-alignstats-505064-20260331-2020-20260425T090724Z/daylily-omics-analysis/results/day/hg38_broad/other_reports/alignstats_gs_mqc.tsv - MultiQC report: pending; no
DAY_final_multiqc.htmlwas found in the checked results report directory.
505451-20260402_1931 <demuxed>
- Run Name:
505451-20260402_1931<demuxed> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN505451/2026/505451-20260402_1931/ - Results S3: pending; no DayOA analysis result directory was found in the checked analysis prefixes.
- Alignstats data: pending.
- MultiQC report: pending.
505799-20260403_1500 <demuxed>
- Run Name:
505799-20260403_1500<demuxed> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN505799/2026/505799-20260403_1500/ - Results S3: pending; no DayOA analysis result directory was found in the checked analysis prefixes.
- Alignstats data: pending.
- MultiQC report: pending.
504352-20260404_1215 <demuxed>
- Run Name:
504352-20260404_1215<demuxed> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN504352/2026/504352-20260404_1215/ - Results S3: pending; no DayOA analysis result directory was found in the checked analysis prefixes.
- Alignstats data: pending.
- MultiQC report: pending.
602220-20260417_2047 <Aligned>
- Run Name:
602220-20260417_2047<Aligned> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN602220/2026/602220-20260417_2047/ - Results S3:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260421T065118Z/analysis_results/ubuntu/prod-alignstats-602220-20260417-2047-20260425T091209Z/daylily-omics-analysis/results/day/hg38_broad/ - Alignstats data:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260421T065118Z/analysis_results/ubuntu/prod-alignstats-602220-20260417-2047-20260425T091209Z/daylily-omics-analysis/results/day/hg38_broad/other_reports/alignstats_gs_mqc.tsv - MultiQC report: pending; no
DAY_final_multiqc.htmlwas found in the checked results report directory.
602221-20260417_2346 <Exception>
- Run Name:
602221-20260417_2346<Exception> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN602221/2026/602221-20260417_2346/ - Source-data issue: current dashboard inventory reports S3 has
1,977,460,351,578bytes versus2,123,313,589,081bytes on SeqNAS, so treat this source prefix as partial until reconciled. - Results S3:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260421T065118Z/analysis_results/ubuntu/prod-alignstats-602221-20260417-2346-20260425T090724Z/daylily-omics-analysis/results/day/hg38_broad/ - Alignstats data:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260421T065118Z/analysis_results/ubuntu/prod-alignstats-602221-20260417-2346-20260425T090724Z/daylily-omics-analysis/results/day/hg38_broad/other_reports/alignstats_gs_mqc.tsv - MultiQC report: pending; no
DAY_final_multiqc.htmlwas found in the checked results report directory.
602202-20260512_1805 <QC complete>
- Run Name:
602202-20260512_1805<QC complete> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/RUN602202/2026/602202-20260512_1805/ - Results S3:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260515T103052Z/analysis_results/ubuntu/ultima_602202_20260512_1805_ksink105_20260517T190121Z/daylily-omics-analysis/results/day/hg38/ - Alignstats data: https://dlqovrcm5y71h.cloudfront.net/ultima_602202_20260512_1805_ksink105_20260517T190121Z/daylily-omics-analysis/results/day/hg38/other_reports/alignstats_gs_mqc.tsv
- MultiQC report: https://dlqovrcm5y71h.cloudfront.net/ultima_602202_20260512_1805_ksink105_20260517T190121Z/daylily-omics-analysis/results/day/hg38/reports/DAY_final_multiqc.html
Illumina
20260507_23andMe_run-1 (0005) <demuxed>
- Run Name:
20260507_23andMe_run-1<demuxed> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260507_LH01106_0005_A23K3JVLT4/ - SampleSheet check: root
SampleSheet.csvhasRunName=20260507_23andMe_run-1, which agrees with this section title for the20260507_LH01106_0005_A23K3JVLT4source directory. - Demux note: BCLConvert report artifacts exist with
93.3175%Q30, but no demux stats file was found in the checked S3 paths. - Results S3: pending; combined-FQ-by-lane run in process.
- Alignstats data: pending; combined-FQ-by-lane run in process.
- MultiQC report: pending; combined-FQ-by-lane run in process.
20260512_ILMN_Altair_Run_1 (0006) <Aligned>
- Run Name:
20260512_ILMN_Altair_Run_1<Aligned> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260512_LH01106_0006_A23K3H2LT4/ - SampleSheet check: root
SampleSheet.csvhasRunName=20260512_ILMN_Altair_Run_1, which agrees with this section title for the20260512_LH01106_0006_A23K3H2LT4source directory. - Demux note: Demux completed and is usable:
85.6783%called reads,14.3217%undetermined reads, all41samples nonzero, and92.9441%Q30. - Results S3:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260515T103052Z/analysis_results/ubuntu/ilmn_0006_align_dedup_alignstats_20260517T185626Z/daylily-omics-analysis/results/day/hg38/ - Alignstats data: https://dlqovrcm5y71h.cloudfront.net/ilmn_0006_align_dedup_alignstats_20260517T185626Z/daylily-omics-analysis/results/day/hg38/other_reports/alignstats_combo_mqc.tsv
- MultiQC report: pending; combined-FQ-by-lane run in process.
20260512_ILMN_Altair_Run_2 (0007) <Exception>
- Run Name:
20260512_ILMN_Altair_Run_2<Exception> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260512_LH01106_0007_B23K5JKLT4/ - SampleSheet check: root
SampleSheet.csvhasRunName=20260512_ILMN_Altair_Run_2, which agrees with this section title for the20260512_LH01106_0007_B23K5JKLT4source directory. - Demux note: Demux artifacts are present, but demux effectively failed: only
8called reads total and almost all reads undetermined despite good sequencing quality. The observed unknown index population does not match the SampleSheet. - Results S3: pending because of the index/demux issue.
- Alignstats data: pending.
- MultiQC report: pending.
20260514_23andMe_run-2 (0008) <in progress>
- Run Name:
20260514_23andMe_run-2<in progress> - Raw data S3:
s3://lsmc-ssf-sequencing-data/raw/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0008_A23TVNWLT4/ - SampleSheet check: root
SampleSheet.csvhasRunName=20260514_23andMe_run-2, which agrees with this section title for the20260514_LH01106_0008_A23TVNWLT4source directory. - Demux note: The raw S3 prefix has
OOW.done, but no demux stats or BCLConvert report CSVs were found in the checked raw prefix. - Results S3: in progress.
- Alignstats data: in progress.
- MultiQC report: in progress.
20260514_ILMN_Altair_Run_3 (0009) <Exception>
- Run Name:
20260514_ILMN_Altair_Run_3<Exception> - Raw data S3:
s3://lsmc-ssf-sequencing-data/raw/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0009_B23TVLGLT4/ - SampleSheet check: root
SampleSheet.csvhasRunName=20260514_ILMN_Altair_Run_3, which agrees with this section title for the20260514_LH01106_0009_B23TVLGLT4source directory. - Demux note: Demux artifacts are present and look usable:
87.0563%called reads,12.9437%undetermined reads, all41samples nonzero, and94.3353%Q30. The raw S3 prefix currently hasOOW.err, so the transfer state should be treated as incomplete or failed until that marker is resolved. - Results S3: pending.
- Alignstats data: pending.
- MultiQC report: pending.
ONT
20260424_ONT_100ul <QC complete>
- Run Name:
20260424_ONT_100ul<QC complete> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/pca100/2026/20260424_ONT_100ul/ - Results S3:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260503T104054Z/analysis_results/ubuntu/pca100_ont_at_sanity_20260504/daylily-omics-analysis/results/day/hg38_broad/ - Alignstats data:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260503T104054Z/analysis_results/ubuntu/pca100_ont_at_sanity_20260504/daylily-omics-analysis/results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv - MultiQC report:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260503T104054Z/analysis_results/ubuntu/pca100_ont_at_sanity_20260504/daylily-omics-analysis/results/day/hg38_broad/reports/DAY_final_multiqc.html - Analysis note: this April ONT result directory includes both
20260424_ONT_100uland20260427_ONT_300ul.
20260427_ONT_300ul <QC complete>
- Run Name:
20260427_ONT_300ul<QC complete> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/pca100/2026/20260427_ONT_300ul/ - Results S3:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260503T104054Z/analysis_results/ubuntu/pca100_ont_at_sanity_20260504/daylily-omics-analysis/results/day/hg38_broad/ - Alignstats data:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260503T104054Z/analysis_results/ubuntu/pca100_ont_at_sanity_20260504/daylily-omics-analysis/results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv - MultiQC report:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260503T104054Z/analysis_results/ubuntu/pca100_ont_at_sanity_20260504/daylily-omics-analysis/results/day/hg38_broad/reports/DAY_final_multiqc.html - Analysis note: this April ONT result directory includes both
20260424_ONT_100uland20260427_ONT_300ul.
20260513_ONT_HG003 <QC complete>
- Run Name:
20260513_ONT_HG003<QC complete> - Raw data S3:
s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/pca100/2026/20260513_ONT_HG003/ - Results S3:
s3://lsmc-dayoa-omics-analysis-us-west-2/FSxLustre20260515T103052Z/analysis_results/ubuntu/pca100_ont_hg003_20260513_kitchen_bc17_unclassified_dryrun2/daylily-omics-analysis/results/day/hg38_broad/ - Alignstats data: https://dlqovrcm5y71h.cloudfront.net/pca100_ont_hg003_20260513_kitchen_bc17_unclassified_dryrun2/daylily-omics-analysis/results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv
- MultiQC report: https://dlqovrcm5y71h.cloudfront.net/pca100_ont_hg003_20260513_kitchen_bc17_unclassified_dryrun2/daylily-omics-analysis/results/day/hg38_broad/reports/DAY_final_multiqc.html
Sample Analysis
Hybrid ILMN+ONT
HG003
<coming soon>