This page contains a list of common ETL issues and its potential solutions.

Missing sample aggregation/BAM file path in PDO Tracker or WGS/WES Project Tracker report

Issue: Missing BAM file path in PDO Tracker or WGS/WES Project Tracker report (PDO_STAR5_Aux DM) (for on-prem only)

Cause:

Seq Only PDOs do not get BAM files in PDO_STAR5_Aux DM
Plated sample in BSP_Plated_Samples is different than slxre_readgroup_metadata.sample_id
Read group of the PDO Sample is missing in SLXRE2_RGHQS, most likely because there isn't a record in metrics.basecall_analysis for metrics_type Indexed or Unindexed.
PM billed sample before PDOSTAR5 picked the most recent aggregation or before sample met full coverage
Determine what is the root cause (using SUPPORT-9123 as an example)

Remedy:

None
Check if Mercury DWH and Mercury Run API still do not agree about the plated sample. If they don't - seek help from Mercury team. If they match, a refresh of the flowcell should correct it. BSP exported samples might be associated with the wrong PDO in BSP_Plated_samples because the mapping in BSP is not accurate. If it is important to fix the data , BSP team could help and then request a refresh for the affected plated sample as instructed in the recipe on this page to update BSP Plating DM. Finally, make sure to refresh in PDO Star5 if it won't happen automatically.
If there is data for Indexed or Unindexed on metrics.basecall_analysis, then the flowcell needs to be refreshed in the datamarts. Otherwise, make ticket for the Pipeline and refer to PO-13231 as being the same issue.
PDOs created within past year will get refreshed on Friday 2:55 am or Analytics manually refresh for faster data delivery. PDOs older than 1 year MUST be manually refreshed. See instructions for PDOSTAR5 refresh in Checking metadata changes.
Steps to determine root cause of missing BAM file path

To view Mercury Run API, add run_name to the end of this query (after 'runName='): https://mercury.broadinstitute.org:8443/Mercury/rest/IlluminaRun/query?runName=190725_SL-NVM_0088_AHKYJVDSXX

Readgroup Metadata refreshes with upstream data change

Issue: When upstream data change, some samples in ReadgroupMetadata might need to be refreshed. For more information, see instructions in Checking metadata changes.

Remedy: Request a refresh for RunMercuryAgent by issuing ~~the following query in SEQPROD.COGNOS~~: RunETL tool

BEGIN
cognos.data_warehouse_api.request_refresh(P_FLOWCELL_BARCODE=>'XYZ1', P_REQUESTED_BY=>'JohnDoe', P_COMMENTS=>'Test', P_DEFERRAL_ANALYSIS_DATE=>null);
cognos.data_warehouse_api.request_refresh(P_FLOWCELL_BARCODE=>'XYZ2', P_REQUESTED_BY=>'JohnDoe', P_COMMENTS=>'Test', P_DEFERRAL_ANALYSIS_DATE=>null);
cognos.data_warehouse_api.request_refresh(P_FLOWCELL_BARCODE=>'XYZ3', P_REQUESTED_BY=>'JohnDoe', P_COMMENTS=>'Test', P_DEFERRAL_ANALYSIS_DATE=>null);
...
cognos.data_warehouse_api.request_refresh(P_FLOWCELL_BARCODE=>'XYZX', P_REQUESTED_BY=>'JohnDoe', P_COMMENTS=>'Test', P_DEFERRAL_ANALYSIS_DATE=>null);
END;

Note: No COMMIT needed in this particular call - it's implicitly done for you. Just replace the XYZ with a flowcell barcode. Leave all other parameters there and unchanged. For more information, see instructions in Checking metadata changes.

PicardAggregator ETL fails with (COGNOS.SLXRE2_PAGG_SAMPLE_PK) violated error

Issue: PicardAggregator ETL fails with (COGNOS.SLXRE2_PAGG_SAMPLE_PK) violated error.

Cause:

Most likely Is_latest flag is set for more than 1 aggregations.
Another case is when samples are reprocessed on the cloud, sample renaming and research project renaming, where the old aggregation needs to be set to "not latest".

Remedy:

There is an agent that looks for certain Is_latest flag violations (IsLatestCop) that specifies the list of metrics.aggregation records with the issues and automatically opens a PO ticket in the pipeline.
Find the sample that causes it (run the query below) and make a blocker PO ticket + notify somebody from Pipeline team to address it ASAP because the ETL won't recover until this is fixed.

SELECT DISTINCT SAMPLEs, agg_ids, proc_loc FROM (
    SELECT  
        rg.flowcell_barcode, rg.lane, rg.molecular_barcode_name, 
        count(DISTINCT a.id ) n,
        concat_string_csv(DISTINCT a.SAMPLE ) samples,
        concat_string_csv(DISTINCT a.id) agg_ids
,        concat_string_csv(DISTINCT a.processing_location) proc_loc
    FROM metrics.aggregation a ,
    metrics.aggregation_read_group rg 
    WHERE 
    a.id = rg.aggregation_id
    AND a.is_latest <> 0 
    AND a.SAMPLE IN (
        SELECT DISTINCT SAMPLE 
        FROM metrics.aggregation a 
        WHERE 
        a.SAMPLE <> 'NA12878'
        AND nvl(a.modified_at, a.workflow_end_date) >= <START DATE FROM ETL dashboard>
        AND nvl(a.modified_at, a.workflow_end_date) < <END DATE FROM ETL dashboard>
    )
    GROUP BY rg.flowcell_barcode, rg.lane, rg.molecular_barcode_name
    HAVING count(DISTINCT a.id )>1
)

Designation ETL fails with "ORA-30926: unable to get a stable set of rows in the source tables" error

Issue: Designation ETL fails with "ORA-30926: unable to get a stable set of rows in the source tables" error

Diagnosis: This is usually caused by a flowcell with 2 runs valid run (uncanceled), one of which should have been cancelled. Run the query below to determine the trouble flowcell:

SELECT r.flowcell_barcode, count(DISTINCT r.run_name)
FROM slxre2_organic_run r
WHERE
r.is_cancelled = 0
AND r.run_type <> 'UNDECIDED'
AND  r.run_date >= <SOME DATE>
GROUP BY r.flowcell_barcode
HAVING count(DISTINCT r.run_name)>1

Remedy: There is an agent (OrganicRun) that reviews if a flowcell has 2 valid runs, and emails the Sequencing team to clear the bad run from their dashboard. Designation ETL will recover as soon as the run is cleared.

Synchronizing data types between metrics tables and Agg DM

Issue: Project sample records may not have the same data type in the Sample and Library level aggregation tables (slxre2_pagg_sample and slxre2_pagg_library).

Cause:

Remedy:

Compare the data types in Sample and Library level aggregations:

SELECT  sa.data_type, a.*
FROM metrics.aggregation a ,
slxre2_pagg_sample sa 
WHERE
a.id = sa.analysis_id
AND  (a.project, a.SAMPLE) IN ( 
('P', 'S'),
...
)
AND a.library IS NULL 
AND a.is_latest <>0
;

SELECT  sa.data_type, a.*
FROM metrics.aggregation a ,
slxre2_pagg_library sa 
WHERE
a.id = sa.analysis_id
AND  (a.project, a.SAMPLE) IN ( 
('P', 'S'),
...
)
AND a.library IS NOT  NULL 
AND a.is_latest <>0
;

Update Analytics DMs

MERGE INTO slxre2_pagg_sample sa 
USING (
    SELECT a.id, a.data_type 
    FROM metrics.aggregation a
    WHERE (a.project, a.SAMPLE) IN ( 
        ('P', 'S'),
        ...
        )
    AND a.library IS NULL 
    AND a.is_latest <>0

) d 
ON (sa.analysis_id = d.id)
WHEN MATCHED THEN UPDATE SET 
sa.data_type = d.data_type 
;
MERGE INTO slxre2_pagg_library sa 
USING (
    SELECT a.id, a.data_type 
    FROM metrics.aggregation a
    WHERE (a.project, a.SAMPLE) IN ( 
        ('P', 'S'),
        ...
        )
    AND a.library IS NOT NULL 
    AND a.is_latest <>0

) d
ON (sa.analysis_id = d.id)
WHEN MATCHED THEN UPDATE SET 
sa.data_type = d.data_type 
;
MERGE INTO slxre2_library_agg_qc sa 
USING (
    SELECT a.id, a.data_type 
    FROM metrics.aggregation a
    WHERE (a.project, a.SAMPLE) IN ( 
        ('P', 'S'),
        ...
        )
    AND a.library IS NOT NULL 
    AND a.is_latest <>0

) d
ON (sa.analysis_id = d.id)
WHEN MATCHED THEN UPDATE SET 
sa.data_type = d.data_type 
;
MERGE INTO slxre2_sample_agg_qc sa 
USING (
    SELECT a.id, a.data_type 
    FROM metrics.aggregation a
    WHERE (a.project, a.SAMPLE) IN ( 
        ('P', 'S'),
        ...
        )
    AND a.library IS NOT NULL 
    AND a.is_latest <>0

) d
ON (sa.analysis_id = d.id)
WHEN MATCHED THEN UPDATE SET 
sa.data_type = d.data_type 
;

Review queries in step 1 to confirm data_type changes.

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