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


Table of Contents


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)

...

  1. Seq Only PDOs do not get BAM files in PDO_STAR5_Aux DM
  2. Plated sample in BSP_Plated_Samples is different than slxre_readgroup_metadata.sample_id
  3. 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.
  4. PM billed sample before PDOSTAR5 picked the most recent aggregation or before sample met full coverage
  5. Determine what is the root cause (using SUPPORT-9123 as an example)

Remedy: 

  1. None
  2. 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.
  3. 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.
  4. 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.
  5. Steps to determine root cause of missing BAM file path
Info

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. Instructions already on Checking Metadata Changes 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

Code Block
languagesql
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;

...

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:

  1. Compare the data types in Sample and Library level aggregations:


    Code Block
    languagesql
    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
;


  2. Update Analytics DMs

    Code Block
    languagesql
    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 
;


  3. Review queries in step 1 to confirm data_type changes.