ETL Stats
Details
ETL run stats for 2022-01-01 to 2022-03-22
ETL Runtimes
*Total processor time, excludes view refreshes and data quality checks
Average Processor Times
All Processor Times
Retries & Errors
Errors for date_tested
2022-01-05 06:48:17
[2022-01-05 06:48:17,216] {{docker_operator.py:243}} INFO - 2022-01-05 06:48:12 INFO [runner.py:121] (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: INSERT INTO master_list.sample_date_tested (sample_id, date_tested) SELECT master_list.sample_id.id AS sample_id, intermediate.sample_date_tested.date_tested FROM intermediate.sample_date_tested JOIN master_list.sample_id ON master_list.sample_id.cog_uk_id = intermediate.sample_date_tested.cog_uk_id OR master_list.sample_id.root_sample_id = intermediate.sample_date_tested.root_sample_id WHERE intermediate.sample_date_tested.date_tested IS NOT NULL ON CONFLICT ON CONSTRAINT date_tested_sample_id_unique DO NOTHING] (Background on this error at: http://sqlalche.me/e/13/e3q8)
2022-01-26 07:10:32
[2022-01-26 07:10:32,456] {{docker_operator.py:243}} INFO - 2022-01-26 07:10:32 INFO [runner.py:121] (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: INSERT INTO master_list.sample_date_tested (sample_id, date_tested) SELECT master_list.sample_id.id AS sample_id, intermediate.sample_date_tested.date_tested FROM intermediate.sample_date_tested JOIN master_list.sample_id ON master_list.sample_id.cog_uk_id = intermediate.sample_date_tested.cog_uk_id OR master_list.sample_id.root_sample_id = intermediate.sample_date_tested.root_sample_id WHERE intermediate.sample_date_tested.date_tested IS NOT NULL ON CONFLICT ON CONSTRAINT date_tested_sample_id_unique DO NOTHING] (Background on this error at: http://sqlalche.me/e/13/e3q8)
2022-01-26 07:10:37
[2022-01-26 07:10:37,469] {{docker_operator.py:243}} INFO - 2022-01-26 07:10:37 INFO [runner.py:130] (MySQLdb._exceptions.OperationalError) (2006, 'MySQL server has gone away')
2022-01-26 07:10:47
[2022-01-26 07:10:47,652] {{docker_operator.py:243}} INFO - 2022-01-26 07:10:37 INFO [runner.py:121] (sqlalchemy.exc.InvalidRequestError) Can't reconnect until invalid transaction is rolled back [SQL: TRUNCATE intermediate.sample_date_tested, master_list.sample_date_tested RESTART IDENTITY;]
2022-01-30 07:17:47
[2022-01-30 07:17:47,529] {{docker_operator.py:243}} INFO - 2022-01-30 07:17:42 INFO [runner.py:121] (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: INSERT INTO master_list.sample_date_tested (sample_id, date_tested) SELECT master_list.sample_id.id AS sample_id, intermediate.sample_date_tested.date_tested FROM intermediate.sample_date_tested JOIN master_list.sample_id ON master_list.sample_id.cog_uk_id = intermediate.sample_date_tested.cog_uk_id OR master_list.sample_id.root_sample_id = intermediate.sample_date_tested.root_sample_id WHERE intermediate.sample_date_tested.date_tested IS NOT NULL ON CONFLICT ON CONSTRAINT date_tested_sample_id_unique DO NOTHING] (Background on this error at: http://sqlalche.me/e/13/e3q8)
2022-01-30 07:17:47
[2022-01-30 07:17:47,529] {{docker_operator.py:243}} INFO - 2022-01-30 07:17:47 INFO [runner.py:130] (MySQLdb._exceptions.OperationalError) (2006, 'MySQL server has gone away')
2022-01-30 07:17:57
[2022-01-30 07:17:57,714] {{docker_operator.py:243}} INFO - 2022-01-30 07:17:47 INFO [runner.py:121] (sqlalchemy.exc.InvalidRequestError) Can't reconnect until invalid transaction is rolled back [SQL: TRUNCATE intermediate.sample_date_tested, master_list.sample_date_tested RESTART IDENTITY;]
2022-02-03 07:22:46
[2022-02-03 07:22:46,537] {{docker_operator.py:243}} INFO - 2022-02-03 07:22:41 INFO [runner.py:121] (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: INSERT INTO master_list.sample_date_tested (sample_id, date_tested) SELECT master_list.sample_id.id AS sample_id, intermediate.sample_date_tested.date_tested FROM intermediate.sample_date_tested JOIN master_list.sample_id ON master_list.sample_id.cog_uk_id = intermediate.sample_date_tested.cog_uk_id OR master_list.sample_id.root_sample_id = intermediate.sample_date_tested.root_sample_id WHERE intermediate.sample_date_tested.date_tested IS NOT NULL ON CONFLICT ON CONSTRAINT date_tested_sample_id_unique DO NOTHING] (Background on this error at: http://sqlalche.me/e/13/e3q8)
2022-02-03 07:22:46
[2022-02-03 07:22:46,537] {{docker_operator.py:243}} INFO - 2022-02-03 07:22:46 INFO [runner.py:130] (MySQLdb._exceptions.OperationalError) (2006, 'MySQL server has gone away')
2022-02-03 07:22:46
[2022-02-03 07:22:46,537] {{docker_operator.py:243}} INFO - 2022-02-03 07:22:46 INFO [runner.py:121] (sqlalchemy.exc.InvalidRequestError) Can't reconnect until invalid transaction is rolled back [SQL: TRUNCATE intermediate.sample_date_tested, master_list.sample_date_tested RESTART IDENTITY;]
Errors for sequencing_start
2022-02-05 06:07:59
[2022-02-05 06:07:59,413] {{docker_operator.py:243}} INFO - 2022-02-05 06:07:54 INFO [runner.py:121] (MySQLdb._exceptions.OperationalError) (2013, 'Lost connection to MySQL server during query') [SQL: SELECT sequence_scape_id, max(sequencing_start) AS sequencing_start, max(sequencing_attempts) AS attempts FROM ( SELECT sample.sanger_sample_id AS sequence_scape_id, MAX(iseq_run_status.date) AS 'sequencing_start', COUNT(DISTINCT iseq_run_status.date) AS 'sequencing_attempts' FROM iseq_flowcell LEFT JOIN iseq_run ON iseq_flowcell.id_flowcell_lims = iseq_run.id_flowcell_lims JOIN study ON iseq_flowcell.id_study_tmp = study.id_study_tmp JOIN sample ON iseq_flowcell.id_sample_tmp = sample.id_sample_tmp LEFT JOIN iseq_run_status ON iseq_run.id_run = iseq_run_status.id_run LEFT JOIN iseq_run_status_dict ON iseq_run_status.id_run_status_dict = iseq_run_status_dict.id_run_status_dict WHERE iseq_run_status_dict.description = 'run pending' AND study.name = 'Heron Project' AND iseq_flowcell.id_study_tmp = 6017 AND ( sample.control = 0 OR sample.control IS NULL ) AND sample.description NOT REGEXP '^RnD:|^.{1,6}$' AND sample.supplier_name NOT LIKE 'Fake_sample_%%' AND sample.supplier_name NOT LIKE 'NEG%%' GROUP BY 1 UNION SELECT sanger_sample_id AS sequence_scape_id, MAX(iseq_run_lane_metrics.run_pending) AS 'sequencing_start', COUNT(distinct iseq_run_lane_metrics.run_pending) AS 'sequencing_runs' FROM sample JOIN iseq_flowcell ON iseq_flowcell.id_sample_tmp = sample.id_sample_tmp JOIN iseq_product_metrics ON iseq_product_metrics.id_iseq_flowcell_tmp = iseq_flowcell.id_iseq_flowcell_tmp JOIN iseq_run_lane_metrics ON iseq_run_lane_metrics.id_run = iseq_product_metrics.id_run AND iseq_run_lane_metrics.position = iseq_product_metrics.position WHERE iseq_flowcell.id_study_tmp = 6017 AND ( sample.control = 0 OR sample.control IS NULL ) AND sample.description NOT REGEXP '^RnD:|^.{1,6}$' AND sample.supplier_name NOT LIKE 'Fake_sample_%%' AND sample.supplier_name NOT LIKE 'NEG%%' GROUP BY 1 ) AS t1 GROUP BY 1 ] (Background on this error at: http://sqlalche.me/e/13/e3q8)
2022-02-09 06:05:36
[2022-02-09 06:05:36,010] {{docker_operator.py:243}} INFO - 2022-02-09 06:05:31 INFO [runner.py:121] (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: INSERT INTO master_list.sequencing_start_fact (sample_id, sequencing_start, attempts) SELECT master_list.sample_id.id AS sample_id, min(intermediate.sequencing_start.sequencing_start) AS sequencing_start, intermediate.sequencing_start.attempts AS attempts FROM master_list.sample_id JOIN intermediate.sequencing_start ON intermediate.sequencing_start.sequence_scape_id = master_list.sample_id.sequence_scape_id GROUP BY intermediate.sequencing_start.attempts, master_list.sample_id.id ON CONFLICT ON CONSTRAINT sequencing_start_fact_pkey DO NOTHING] (Background on this error at: http://sqlalche.me/e/13/e3q8)
2022-02-09 06:05:36
[2022-02-09 06:05:36,010] {{docker_operator.py:243}} INFO - 2022-02-09 06:05:36 INFO [runner.py:130] (MySQLdb._exceptions.OperationalError) (2006, 'MySQL server has gone away')
2022-02-09 06:05:36
[2022-02-09 06:05:36,011] {{docker_operator.py:243}} INFO - 2022-02-09 06:05:36 INFO [runner.py:121] (sqlalchemy.exc.InvalidRequestError) Can't reconnect until invalid transaction is rolled back [SQL: TRUNCATE intermediate.sequencing_start, master_list.sequencing_start_fact RESTART IDENTITY;]
2022-02-10 06:08:11
[2022-02-10 06:08:11,039] {{docker_operator.py:243}} INFO - 2022-02-10 06:08:11 INFO [runner.py:121] (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: INSERT INTO intermediate.sequencing_start (sequence_scape_id, sequencing_start, attempts) VALUES (%(sequence_scape_id_m0)s, %(sequencing_start_m0)s, %(attempts_m0)s), (%(sequence_scape_id_m1)s, %(sequencing_start_m1)s, %(attempts_m1)s), (%(sequence_scape_id_m2)s, %(sequencing_start_m2)s, %(attempts_m2)s), (%(sequence_scape_id_m3)s, %(sequencing_start_m3)s, %(attempts_m3)s), (%(sequence_scape_id_m4)s, %(sequencing_start_m4)s, %(attempts_m4)s), (%(sequence_scape_id_m5)s, %(sequencing_start_m5)s, %(attempts_m5)s), (%(sequence_scape_id_m6)s, %(sequencing_start_m6)s, %(attempts_m6)s), (%(sequence_scape_id_m7)s, %(sequencing_start_m7)s, %(attempts_m7)s), (%(sequence_scape_id_m8)s, %(sequencing_start_m8)s, %(attempts_m8)s), (%(sequence_scape_id_m9)s, %(sequencing_start_m9)s, %(attempts_m9)s), (%(sequence_scape_id_m10)s, %(sequencing_start_m10)s, %(attempts_m10)s), (%(sequence_scape_id_m11)s, %(sequencing_start_m11)s, %(attempts_m11)s), (%(sequence_scape_id_m12)s, %(sequencing_start_m12)s, %(attempts_m12)s), (%(sequence_scape_id_m13)s, %(sequencing_start_m13)s, %(attempts_m13)s), (%(sequence_scape_id_m14)s, %(sequencing_start_m14)s, %(attempts_m14)s), (%(sequence_scape_id_m15)s, %(sequencing_start_m15)s, %(attempts_m15)s), (%(sequence_scape_id_m16)s, %(sequencing_start_m16)s, %(attempts_m16)s), (%(sequence_scape_id_m17)s, %(sequencing_start_m17)s, %(attempts_m17)s), (%(sequence_scape_id_m18)s, %(sequencing_start_m18)s, %(attempts_m18)s), (%(sequence_scape_id_m19)s, %(sequencing_start_m19)s, %(attempts_m19)s), (%(sequence_scape_id_m20)s, %(sequencing_start_m20)s, %(attempts_m20)s), (%(sequence_scape_id_m21)s, %(sequencing_start_m21)s, %(attempts_m21)s), (%(sequence_scape_id_m22)s, %(sequencing_start_m22)s, %(attempts_m22)s), (%(sequence_scape_id_m23)s, %(sequencing_start_m23)s, %(attempts_m23)s), (%(sequence_scape_id_m24)s, %(sequencing_start_m24)s, %(attempts_m24)s), (%(sequence_scape_id_m25)s, %(sequencing_start_m25)s, %(attempts_m25)s), (%(sequence_scape_id_m26)s, %(sequencing_start_m26)s, %(attempts_m26)s), (%(sequence_scape_id_m27)s, %(sequencing_start_m27)s, %(attempts_m27)s), (%(sequence_scape_id_m28)s, %(sequencing_start_m28)s, %(attempts_m28)s), (%(sequence_scape_id_m29)s, %(sequencing_start_m29)s, %(attempts_m29)s), (%(sequence_scape_id_m30)s, %(sequencing_start_m30)s, %(attempts_m30)s), (%(sequence_scape_id_m31)s, %(sequencing_start_m31)s, %(attempts_m31)s), (%(sequence_scape_id_m32)s, %(sequencing_start_m32)s, %(attempts_m32)s), (%(sequence_scape_id_m33)s, %(sequencing_start_m33)s, %(attempts_m33)s), (%(sequence_scape_id_m34)s, %(sequencing_start_m34)s, %(attempts_m34)s), (%(sequence_scape_id_m35)s, %(sequencing_start_m35)s, %(attempts_m35)s), (%(sequence_scape_id_m36)s, %(sequencing_start_m36)s, %(attempts_m36)s), (%(sequence_scape_id_m37)s, %(sequencing_start_m37)s, %(attempts_m37)s), (%(sequence_scape_id_m38)s, %(sequencing_start_m38)s, %(attempts_m38)s), (%(sequence_scape_id_m39)s, %(sequencing_start_m39)s, %(attempts_m39)s), (%(sequence_scape_id_m40)s, %(sequencing_start_m40)s, %(attempts_m40)s), (%(sequence_scape_id_m41)s, %(sequencing_start_m41)s, %(attempts_m41)s), (%(sequence_scape_id_m42)s, %(sequencing_start_m42)s, %(attempts_m42)s), (%(sequence_scape_id_m43)s, %(sequencing_start_m43)s, %(attempts_m43)s), (%(sequence_scape_id_m44)s, %(sequencing_start_m44)s, %(attempts_m44)s), (%(sequence_scape_id_m45)s, %(sequencing_start_m45)s, %(attempts_m45)s), (%(sequence_scape_id_m46)s, %(sequencing_start_m46)s, %(attempts_m46)s), (%(sequence_scape_id_m47)s, %(sequencing_start_m47)s, %(attempts_m47)s), (%(sequence_scape_id_m48)s, %(sequencing_start_m48)s, %(attempts_m48)s), (%(sequence_scape_id_m49)s, %(sequencing_start_m49)s, %(attempts_m49)s), (%(sequence_scape_id_m50)s, %(sequencing_start_m50)s, %(attempts_m50)s), (%(sequence_scape_id_m51)s,...
2022-02-10 06:08:16
[2022-02-10 06:08:16,051] {{docker_operator.py:243}} INFO - 2022-02-10 06:08:16 INFO [runner.py:130] (MySQLdb._exceptions.OperationalError) (2006, 'MySQL server has gone away')
2022-02-10 06:08:16
[2022-02-10 06:08:16,051] {{docker_operator.py:243}} INFO - 2022-02-10 06:08:16 INFO [runner.py:121] (sqlalchemy.exc.InvalidRequestError) Can't reconnect until invalid transaction is rolled back [SQL: TRUNCATE intermediate.sequencing_start, master_list.sequencing_start_fact RESTART IDENTITY;]
Errors for sample
2022-02-17 05:03:56
[2022-02-17 05:03:56,460] {{docker_operator.py:243}} INFO - 2022-02-17 05:03:56 INFO [runner.py:121] (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: INSERT INTO master_list.sample_id (id, uuid_sample_lims, root_sample_id, cog_uk_id, sequence_scape_id, rna_id, ch1_target, ch2_target, ch3_target, ch1_result, ch2_result, ch3_result, ch1_cq, ch2_cq, ch3_cq) SELECT uuid_generate_v5(%(uuid_generate_v5_1)s, concat_ws(%(concat_ws_1)s, coalesce(coalesce(lighthouse_samples.root_sample_id, mlwh_samples.root_sample_id), %(coalesce_1)s), coalesce(coalesce(lighthouse_samples.cog_uk_id, mlwh_samples.cog_uk_id), %(coalesce_2)s), coalesce(coalesce(lighthouse_samples.sequence_scape_id, mlwh_samples.sequence_scape_id), %(coalesce_3)s), coalesce(coalesce(lighthouse_samples.rna_id, mlwh_samples.rna_id), %(coalesce_4)s))) AS id, coalesce(lighthouse_samples.uuid_sample_lims, mlwh_samples.uuid_sample_lims) AS uuid_sample_lims, coalesce(lighthouse_samples.root_sample_id, mlwh_samples.root_sample_id) AS root_sample_id, coalesce(lighthouse_samples.cog_uk_id, mlwh_samples.cog_uk_id) AS cog_uk_id, coalesce(lighthouse_samples.sequence_scape_id, mlwh_samples.sequence_scape_id) AS sequence_scape_id, coalesce(lighthouse_samples.rna_id, mlwh_samples.rna_id) AS rna_id, intermediate.sample_result.ch1_target AS ch1_target, intermediate.sample_result.ch2_target AS ch2_target, intermediate.sample_result.ch3_target AS ch3_target, intermediate.sample_result.ch1_result AS ch1_result, intermediate.sample_result.ch2_result AS ch2_result, intermediate.sample_result.ch3_result AS ch3_result, intermediate.sample_result.ch1_cq AS ch1_cq, intermediate.sample_result.ch2_cq AS ch2_cq, intermediate.sample_result.ch3_cq AS ch3_cq FROM (SELECT intermediate.sample_id.id AS id, intermediate.sample_id.cog_uk_id AS cog_uk_id, intermediate.sample_id.root_sample_id AS root_sample_id, intermediate.sample_id.sequence_scape_id AS sequence_scape_id, intermediate.sample_id.rna_id AS rna_id, intermediate.sample_id.uuid_sample_lims AS uuid_sample_lims FROM intermediate.sample_id WHERE intermediate.sample_id.rna_id IS NOT NULL) AS lighthouse_samples FULL OUTER JOIN (SELECT intermediate.sample_id.id AS id, intermediate.sample_id.cog_uk_id AS cog_uk_id, intermediate.sample_id.root_sample_id AS root_sample_id, intermediate.sample_id.sequence_scape_id AS sequence_scape_id, intermediate.sample_id.rna_id AS rna_id, intermediate.sample_id.uuid_sample_lims AS uuid_sample_lims FROM intermediate.sample_id WHERE intermediate.sample_id.rna_id IS NULL) AS mlwh_samples ON mlwh_samples.cog_uk_id = lighthouse_samples.cog_uk_id AND mlwh_samples.root_sample_id = lighthouse_samples.root_sample_id OR mlwh_samples.cog_uk_id = lighthouse_samples.cog_uk_id AND mlwh_samples.root_sample_id IS NULL LEFT OUTER JOIN intermediate.sample_result ON lighthouse_samples.rna_id = intermediate.sample_result.rna_id ON CONFLICT ON CONSTRAINT sample_id_pkey DO NOTHING] [parameters: {'uuid_generate_v5_1': '51043b3e-7877-4da0-828f-b225920b5796', 'concat_ws_1': '-', 'coalesce_1': 'None', 'coalesce_2': 'None', 'coalesce_3': 'None', 'coalesce_4': 'None'}] (Background on this error at: http://sqlalche.me/e/13/e3q8)
2022-02-18 04:19:56
[2022-02-18 04:19:56,638] {{docker_operator.py:243}} INFO - 2022-02-18 04:19:51 INFO [runner.py:121] (MySQLdb._exceptions.OperationalError) (2013, 'Lost connection to MySQL server during query') [SQL: SELECT sample.supplier_name AS cog_uk_id, sample.sanger_sample_id AS sequence_scape_id, CASE WHEN (NOT (substring(sample.supplier_name, %s, %s) IN (%s, %s) OR substring(sample.supplier_name, %s, %s) IN (%s, %s))) THEN sample.description END AS root_sample_id, sample.uuid_sample_lims AS uuid_sample_lims FROM sample INNER JOIN stock_resource ON stock_resource.id_study_tmp = %s AND stock_resource.id_sample_tmp = sample.id_sample_tmp WHERE (sample.control IS false OR sample.control IS NULL) AND sample.supplier_name NOT LIKE %s AND sample.supplier_name NOT LIKE %s AND sample.description NOT LIKE %s AND length(sample.description) > %s] [parameters: (1, 5, 'BRIS-', 'CAMB-', 1, 3, 'POS', 'NEG', 6017, 'Fake_sample_%', 'NEG%', 'RnD:%', 6)] (Background on this error at: http://sqlalche.me/e/13/e3q8)
2022-02-21 04:18:31
[2022-02-21 04:18:31,696] {{docker_operator.py:243}} INFO - 2022-02-21 04:18:26 INFO [runner.py:121] (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: INSERT INTO intermediate.sample_id (cog_uk_id, root_sample_id, rna_id) VALUES (%(cog_uk_id_m0)s, %(root_sample_id_m0)s, %(rna_id_m0)s), (%(cog_uk_id_m1)s, %(root_sample_id_m1)s, %(rna_id_m1)s), (%(cog_uk_id_m2)s, %(root_sample_id_m2)s, %(rna_id_m2)s), (%(cog_uk_id_m3)s, %(root_sample_id_m3)s, %(rna_id_m3)s), (%(cog_uk_id_m4)s, %(root_sample_id_m4)s, %(rna_id_m4)s), (%(cog_uk_id_m5)s, %(root_sample_id_m5)s, %(rna_id_m5)s), (%(cog_uk_id_m6)s, %(root_sample_id_m6)s, %(rna_id_m6)s), (%(cog_uk_id_m7)s, %(root_sample_id_m7)s, %(rna_id_m7)s), (%(cog_uk_id_m8)s, %(root_sample_id_m8)s, %(rna_id_m8)s), (%(cog_uk_id_m9)s, %(root_sample_id_m9)s, %(rna_id_m9)s), (%(cog_uk_id_m10)s, %(root_sample_id_m10)s, %(rna_id_m10)s), (%(cog_uk_id_m11)s, %(root_sample_id_m11)s, %(rna_id_m11)s), (%(cog_uk_id_m12)s, %(root_sample_id_m12)s, %(rna_id_m12)s), (%(cog_uk_id_m13)s, %(root_sample_id_m13)s, %(rna_id_m13)s), (%(cog_uk_id_m14)s, %(root_sample_id_m14)s, %(rna_id_m14)s), (%(cog_uk_id_m15)s, %(root_sample_id_m15)s, %(rna_id_m15)s), (%(cog_uk_id_m16)s, %(root_sample_id_m16)s, %(rna_id_m16)s), (%(cog_uk_id_m17)s, %(root_sample_id_m17)s, %(rna_id_m17)s), (%(cog_uk_id_m18)s, %(root_sample_id_m18)s, %(rna_id_m18)s), (%(cog_uk_id_m19)s, %(root_sample_id_m19)s, %(rna_id_m19)s), (%(cog_uk_id_m20)s, %(root_sample_id_m20)s, %(rna_id_m20)s), (%(cog_uk_id_m21)s, %(root_sample_id_m21)s, %(rna_id_m21)s), (%(cog_uk_id_m22)s, %(root_sample_id_m22)s, %(rna_id_m22)s), (%(cog_uk_id_m23)s, %(root_sample_id_m23)s, %(rna_id_m23)s), (%(cog_uk_id_m24)s, %(root_sample_id_m24)s, %(rna_id_m24)s), (%(cog_uk_id_m25)s, %(root_sample_id_m25)s, %(rna_id_m25)s), (%(cog_uk_id_m26)s, %(root_sample_id_m26)s, %(rna_id_m26)s), (%(cog_uk_id_m27)s, %(root_sample_id_m27)s, %(rna_id_m27)s), (%(cog_uk_id_m28)s, %(root_sample_id_m28)s, %(rna_id_m28)s), (%(cog_uk_id_m29)s, %(root_sample_id_m29)s, %(rna_id_m29)s), (%(cog_uk_id_m30)s, %(root_sample_id_m30)s, %(rna_id_m30)s), (%(cog_uk_id_m31)s, %(root_sample_id_m31)s, %(rna_id_m31)s), (%(cog_uk_id_m32)s, %(root_sample_id_m32)s, %(rna_id_m32)s), (%(cog_uk_id_m33)s, %(root_sample_id_m33)s, %(rna_id_m33)s), (%(cog_uk_id_m34)s, %(root_sample_id_m34)s, %(rna_id_m34)s), (%(cog_uk_id_m35)s, %(root_sample_id_m35)s, %(rna_id_m35)s), (%(cog_uk_id_m36)s, %(root_sample_id_m36)s, %(rna_id_m36)s), (%(cog_uk_id_m37)s, %(root_sample_id_m37)s, %(rna_id_m37)s), (%(cog_uk_id_m38)s, %(root_sample_id_m38)s, %(rna_id_m38)s), (%(cog_uk_id_m39)s, %(root_sample_id_m39)s, %(rna_id_m39)s), (%(cog_uk_id_m40)s, %(root_sample_id_m40)s, %(rna_id_m40)s), (%(cog_uk_id_m41)s, %(root_sample_id_m41)s, %(rna_id_m41)s), (%(cog_uk_id_m42)s, %(root_sample_id_m42)s, %(rna_id_m42)s), (%(cog_uk_id_m43)s, %(root_sample_id_m43)s, %(rna_id_m43)s), (%(cog_uk_id_m44)s, %(root_sample_id_m44)s, %(rna_id_m44)s), (%(cog_uk_id_m45)s, %(root_sample_id_m45)s, %(rna_id_m45)s), (%(cog_uk_id_m46)s, %(root_sample_id_m46)s, %(rna_id_m46)s), (%(cog_uk_id_m47)s, %(root_sample_id_m47)s, %(rna_id_m47)s), (%(cog_uk_id_m48)s, %(root_sample_id_m48)s, %(rna_id_m48)s), (%(cog_uk_id_m49)s, %(root_sample_id_m49)s, %(rna_id_m49)s), (%(cog_uk_id_m50)s, %(root_sample_id_m50)s, %(rna_id_m50)s), (%(cog_uk_id_m51)s, %(root_sample_id_m51)s, %(rna_id_m51)s), (%(cog_uk_id_m52)s, %(root_sample_id_m52)s, %(rna_id_m52)s), (%(cog_uk_id_m53)s, %(root_sample_id_m53)s, %(rna_id_m53)s), (%(cog_uk_id_m54)s, %(root_sample_id_m54)s, %(rna_id_m54)s), (%(cog_uk_id_m55)s, %(root_sample_id_m55)s, %(rna_id_m55)s), (%(cog_uk_id_m56)s, %(root_sample_id_m56)s, %(rna_id_m56)s), (%(cog_uk_id_m57)s, %(root_sample_id_m57)s, %(rna_id_m57)s), (%(cog_uk_id_m58)s, %(root_sample_id_m58)s, %(rna_id_m58)s), (%(cog_uk_id_m59)s, %(root_sample_id_m59)s, %(rna_id_m59)s), (%(cog_uk_id_m60)s, %(root_sample_id_m60)s, %(rna_id_m60)s), (%(cog_uk_id_m61)s, %(root_sample_id_m61)s,...
2022-02-21 04:18:31
[2022-02-21 04:18:31,697] {{docker_operator.py:243}} INFO - 2022-02-21 04:18:31 INFO [runner.py:130] (MySQLdb._exceptions.OperationalError) (2006, 'MySQL server has gone away')
2022-02-21 04:18:41
[2022-02-21 04:18:41,883] {{docker_operator.py:243}} INFO - 2022-02-21 04:18:31 INFO [runner.py:121] (sqlalchemy.exc.InvalidRequestError) Can't reconnect until invalid transaction is rolled back [SQL: TRUNCATE master_list.sample_id, intermediate.sample_id, intermediate.sample_result, master_list.plate_destroyed RESTART IDENTITY;]
2022-02-22 04:22:44
[2022-02-22 04:22:44,507] {{docker_operator.py:243}} INFO - 2022-02-22 04:22:39 INFO [runner.py:121] (MySQLdb._exceptions.OperationalError) (2013, 'Lost connection to MySQL server during query') [SQL: select lighthouse_sample.rna_id, lighthouse_sample.ch1_target, lighthouse_sample.ch2_target, lighthouse_sample.ch3_target, lighthouse_sample.ch1_result, lighthouse_sample.ch2_result, lighthouse_sample.ch3_result, lighthouse_sample.ch1_cq, lighthouse_sample.ch2_cq, lighthouse_sample.ch3_cq from lighthouse_sample join (select rna_id, MAX(id) as latest_insert from lighthouse_sample where result = 'Positive' group by rna_id ) as most_recent on most_recent.rna_id = lighthouse_sample.rna_id and most_recent.latest_insert = lighthouse_sample.id where lighthouse_sample.result = 'Positive' and lighthouse_sample.root_sample_id not REGEXP '^RnD:|^.{1,6}$'] (Background on this error at: http://sqlalche.me/e/13/e3q8)
Errors for plate_map_received
2022-03-13 07:40:32
[2022-03-13 07:40:32,740] {{docker_operator.py:243}} INFO - 2022-03-13 07:40:32 INFO [runner.py:121] (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: REFRESH MATERIALIZED VIEW master_list.sample_fact] (Background on this error at: http://sqlalche.me/e/13/e3q8)
2022-03-13 07:40:37
[2022-03-13 07:40:37,818] {{docker_operator.py:243}} INFO - 2022-03-13 07:40:37 INFO [runner.py:130] (MySQLdb._exceptions.OperationalError) (2006, 'MySQL server has gone away')
2022-03-13 08:38:54
[2022-03-13 08:38:54,895] {{docker_operator.py:243}} INFO - 2022-03-13 07:40:37 INFO [runner.py:121] (sqlalchemy.exc.InvalidRequestError) Can't reconnect until invalid transaction is rolled back [SQL: REFRESH MATERIALIZED VIEW master_list.sample_fact] [parameters: [{}]]
2022-03-16 07:48:06
[2022-03-16 07:48:06,341] {{docker_operator.py:243}} INFO - 2022-03-16 07:48:06 INFO [runner.py:121] (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: REFRESH MATERIALIZED VIEW master_list.sample_fact] (Background on this error at: http://sqlalche.me/e/13/e3q8)
2022-03-16 07:48:11
[2022-03-16 07:48:11,388] {{docker_operator.py:243}} INFO - 2022-03-16 07:48:11 INFO [runner.py:130] (MySQLdb._exceptions.OperationalError) (2006, 'MySQL server has gone away')
2022-03-16 07:48:11
[2022-03-16 07:48:11,388] {{docker_operator.py:243}} INFO - 2022-03-16 07:48:11 INFO [runner.py:121] (sqlalchemy.exc.InvalidRequestError) Can't reconnect until invalid transaction is rolled back [SQL: REFRESH MATERIALIZED VIEW master_list.sample_fact] [parameters: [{}]]
2022-03-17 07:41:09
[2022-03-17 07:41:09,509] {{docker_operator.py:243}} INFO - 2022-03-17 07:41:09 INFO [runner.py:121] (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: REFRESH MATERIALIZED VIEW master_list.sample_fact] (Background on this error at: http://sqlalche.me/e/13/e3q8)
2022-03-17 07:41:14
[2022-03-17 07:41:14,522] {{docker_operator.py:243}} INFO - 2022-03-17 07:41:14 INFO [runner.py:130] (MySQLdb._exceptions.OperationalError) (2006, 'MySQL server has gone away')
2022-03-17 07:41:14
[2022-03-17 07:41:14,522] {{docker_operator.py:243}} INFO - 2022-03-17 07:41:14 INFO [runner.py:121] (sqlalchemy.exc.InvalidRequestError) Can't reconnect until invalid transaction is rolled back [SQL: REFRESH MATERIALIZED VIEW master_list.sample_fact] [parameters: [{}]]
2022-03-21 07:59:14
[2022-03-21 07:59:14,976] {{docker_operator.py:243}} INFO - 2022-03-21 07:59:14 INFO [runner.py:121] (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: REFRESH MATERIALIZED VIEW master_list.sample_fact] (Background on this error at: http://sqlalche.me/e/13/e3q8)
2022-03-21 07:59:19
[2022-03-21 07:59:19,999] {{docker_operator.py:243}} INFO - 2022-03-21 07:59:19 INFO [runner.py:130] (MySQLdb._exceptions.OperationalError) (2006, 'MySQL server has gone away')
2022-03-21 08:54:07
[2022-03-21 08:54:07,943] {{docker_operator.py:243}} INFO - 2022-03-21 07:59:19 INFO [runner.py:121] (sqlalchemy.exc.InvalidRequestError) Can't reconnect until invalid transaction is rolled back [SQL: REFRESH MATERIALIZED VIEW master_list.sample_fact] [parameters: [{}]]