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Clinical-Genomics / trailblazer

Keep track of and manage analyses
MIT License
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feat(sql): Rename sars-cov-2 to mutant #359

Closed henrikstranneheim closed 8 months ago

henrikstranneheim commented 8 months ago

Description

Added

-

Changed

Fixed

-

How to prepare for test

How to test

Expected test outcome

Review

This version is a

henrikstranneheim commented 8 months ago

Db πŸ‘

Screenshot 2024-01-19 at 13 38 34
henrikstranneheim commented 8 months ago

cg workflow mutant start frankhusky πŸ‘

[henrik.stranneheim@hasta:~] [S_base] $ cg workflow mutant start frankhusky
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Found file ACC7703A1/2021-03-18/H3YY3DRXY_395698_S76_L001_R1_001.fastq.gz
Found file ACC7703A1/2021-03-18/H3YY3DRXY_395698_S76_L002_R2_001.fastq.gz
Found file ACC7703A1/2021-03-18/H3YY3DRXY_395698_S76_L001_R2_001.fastq.gz
Found file ACC7703A1/2021-03-18/H3YY3DRXY_395698_S76_L002_R1_001.fastq.gz
Found file ACC7703A2/2021-03-18/H3YY3DRXY_395698_S84_L002_R1_001.fastq.gz
Found file ACC7703A2/2021-03-18/H3YY3DRXY_395698_S84_L001_R2_001.fastq.gz
Found file ACC7703A2/2021-03-18/H3YY3DRXY_395698_S84_L002_R2_001.fastq.gz
Found file ACC7703A2/2021-03-18/H3YY3DRXY_395698_S84_L001_R1_001.fastq.gz
Found file ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L003_R2_001.fastq.gz
Found file ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L004_R2_001.fastq.gz
Found file ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L001_R1_001.fastq.gz
Found file ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L002_R2_001.fastq.gz
Found file ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L004_R1_001.fastq.gz
Found file ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L003_R1_001.fastq.gz
Found file ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L002_R1_001.fastq.gz
Found file ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L001_R2_001.fastq.gz
Found file ACC7703A3/2021-03-18/H3YY3DRXY_395698_S92_L002_R1_001.fastq.gz
Found file ACC7703A3/2021-03-18/H3YY3DRXY_395698_S92_L001_R1_001.fastq.gz
Found file ACC7703A3/2021-03-18/H3YY3DRXY_395698_S92_L002_R2_001.fastq.gz
Found file ACC7703A3/2021-03-18/H3YY3DRXY_395698_S92_L001_R2_001.fastq.gz
Found file ACC7703A4/2021-03-18/H3YY3DRXY_395698_S100_L002_R2_001.fastq.gz
Found file ACC7703A4/2021-03-18/H3YY3DRXY_395698_S100_L001_R2_001.fastq.gz
Found file ACC7703A4/2021-03-18/H3YY3DRXY_395698_S100_L002_R1_001.fastq.gz
Found file ACC7703A4/2021-03-18/H3YY3DRXY_395698_S100_L001_R1_001.fastq.gz
Found file ACC7703A5/2021-03-18/H3YY3DRXY_395698_S108_L002_R1_001.fastq.gz
Found file ACC7703A5/2021-03-18/H3YY3DRXY_395698_S108_L002_R2_001.fastq.gz
Found file ACC7703A5/2021-03-18/H3YY3DRXY_395698_S108_L001_R1_001.fastq.gz
Found file ACC7703A5/2021-03-18/H3YY3DRXY_395698_S108_L001_R2_001.fastq.gz
Found file ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L002_R2_001.fastq.gz
Found file ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L004_R2_001.fastq.gz
Found file ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L003_R1_001.fastq.gz
Found file ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L001_R1_001.fastq.gz
Found file ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L004_R1_001.fastq.gz
Found file ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L002_R1_001.fastq.gz
Found file ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L001_R2_001.fastq.gz
Found file ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L003_R2_001.fastq.gz
Found file ACC7703A6/2021-03-18/H3YY3DRXY_395698_S115_L001_R2_001.fastq.gz
Found file ACC7703A6/2021-03-18/H3YY3DRXY_395698_S115_L002_R1_001.fastq.gz
Found file ACC7703A6/2021-03-18/H3YY3DRXY_395698_S115_L002_R2_001.fastq.gz
Found file ACC7703A6/2021-03-18/H3YY3DRXY_395698_S115_L001_R1_001.fastq.gz
Found file ACC7703A7/2021-03-18/H3YY3DRXY_395698_S122_L002_R1_001.fastq.gz
Found file ACC7703A7/2021-03-18/H3YY3DRXY_395698_S122_L002_R2_001.fastq.gz
Found file ACC7703A7/2021-03-18/H3YY3DRXY_395698_S122_L001_R1_001.fastq.gz
Found file ACC7703A7/2021-03-18/H3YY3DRXY_395698_S122_L001_R2_001.fastq.gz
Found file ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L002_R1_001.fastq.gz
Found file ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L004_R2_001.fastq.gz
Found file ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L003_R1_001.fastq.gz
Found file ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L002_R2_001.fastq.gz
Found file ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L003_R2_001.fastq.gz
Found file ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L004_R1_001.fastq.gz
Found file ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L001_R1_001.fastq.gz
Found file ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L001_R2_001.fastq.gz
Found file ACC7703A8/2021-03-18/H3YY3DRXY_395698_S129_L001_R2_001.fastq.gz
Found file ACC7703A8/2021-03-18/H3YY3DRXY_395698_S129_L002_R1_001.fastq.gz
Found file ACC7703A8/2021-03-18/H3YY3DRXY_395698_S129_L001_R1_001.fastq.gz
Found file ACC7703A8/2021-03-18/H3YY3DRXY_395698_S129_L002_R2_001.fastq.gz
Found file ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L002_R2_001.fastq.gz
Found file ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L002_R1_001.fastq.gz
Found file ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L003_R2_001.fastq.gz
Found file ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L003_R1_001.fastq.gz
Found file ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L004_R1_001.fastq.gz
Found file ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L001_R1_001.fastq.gz
Found file ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L004_R2_001.fastq.gz
Found file ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L001_R2_001.fastq.gz
Found file ACC7703A9/2021-03-18/H3YY3DRXY_395698_S77_L001_R2_001.fastq.gz
Found file ACC7703A9/2021-03-18/H3YY3DRXY_395698_S77_L002_R2_001.fastq.gz
Found file ACC7703A9/2021-03-18/H3YY3DRXY_395698_S77_L001_R1_001.fastq.gz
Found file ACC7703A9/2021-03-18/H3YY3DRXY_395698_S77_L002_R1_001.fastq.gz
Found file ACC7703A10/2021-03-18/H3YY3DRXY_395698_S85_L002_R1_001.fastq.gz
Found file ACC7703A10/2021-03-18/H3YY3DRXY_395698_S85_L002_R2_001.fastq.gz
Found file ACC7703A10/2021-03-18/H3YY3DRXY_395698_S85_L001_R2_001.fastq.gz
Found file ACC7703A10/2021-03-18/H3YY3DRXY_395698_S85_L001_R1_001.fastq.gz
Found file ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L001_R2_001.fastq.gz
Found file ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L004_R2_001.fastq.gz
Found file ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L004_R1_001.fastq.gz
Found file ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L003_R1_001.fastq.gz
Found file ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L002_R2_001.fastq.gz
Found file ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L003_R2_001.fastq.gz
Found file ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L001_R1_001.fastq.gz
Found file ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L002_R1_001.fastq.gz
Found file ACC7703A11/2021-03-18/H3YY3DRXY_395698_S93_L001_R2_001.fastq.gz
Found file ACC7703A11/2021-03-18/H3YY3DRXY_395698_S93_L002_R1_001.fastq.gz
Found file ACC7703A11/2021-03-18/H3YY3DRXY_395698_S93_L001_R1_001.fastq.gz
Found file ACC7703A11/2021-03-18/H3YY3DRXY_395698_S93_L002_R2_001.fastq.gz
Found file ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L004_R2_001.fastq.gz
Found file ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L003_R1_001.fastq.gz
Found file ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L001_R2_001.fastq.gz
Found file ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L003_R2_001.fastq.gz
Found file ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L002_R1_001.fastq.gz
Found file ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L001_R1_001.fastq.gz
Found file ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L004_R1_001.fastq.gz
Found file ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L002_R2_001.fastq.gz
Found file ACC7703A12/2021-03-18/H3YY3DRXY_395698_S101_L001_R2_001.fastq.gz
Found file ACC7703A12/2021-03-18/H3YY3DRXY_395698_S101_L002_R2_001.fastq.gz
Found file ACC7703A12/2021-03-18/H3YY3DRXY_395698_S101_L001_R1_001.fastq.gz
Found file ACC7703A12/2021-03-18/H3YY3DRXY_395698_S101_L002_R1_001.fastq.gz
Case frankhusky exists in Status DB
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A1/2021-03-18/H3YY3DRXY_395698_S76_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500657TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A1/2021-03-18/H3YY3DRXY_395698_S76_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500657TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A1/2021-03-18/H3YY3DRXY_395698_S76_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500657TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A1/2021-03-18/H3YY3DRXY_395698_S76_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500657TEST_2.fastq.gz
Concatenation in progress for sample: ACC7703A1
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500657TEST_1.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500657TEST_1.fastq.gz -> 01_SE100_21CS500657TEST_1.fastq.gz
Concatenation file size check successful!
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500657TEST_2.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500657TEST_2.fastq.gz -> 01_SE100_21CS500657TEST_2.fastq.gz
Concatenation file size check successful!
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A2/2021-03-18/H3YY3DRXY_395698_S84_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500658TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A2/2021-03-18/H3YY3DRXY_395698_S84_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500658TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A2/2021-03-18/H3YY3DRXY_395698_S84_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500658TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A2/2021-03-18/H3YY3DRXY_395698_S84_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500658TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L1_01_SE100_21CS500658TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L1_01_SE100_21CS500658TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L2_01_SE100_21CS500658TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L2_01_SE100_21CS500658TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L003_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L3_01_SE100_21CS500658TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L003_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L3_01_SE100_21CS500658TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L004_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L4_01_SE100_21CS500658TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A2/2021-03-18/HN33FDSXY_395698_S3_L004_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L4_01_SE100_21CS500658TEST_2.fastq.gz
Concatenation in progress for sample: ACC7703A2
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500658TEST_1.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500658TEST_1.fastq.gz, HN33FDSXY_L1_01_SE100_21CS500658TEST_1.fastq.gz, HN33FDSXY_L2_01_SE100_21CS500658TEST_1.fastq.gz, HN33FDSXY_L3_01_SE100_21CS500658TEST_1.fastq.gz, HN33FDSXY_L4_01_SE100_21CS500658TEST_1.fastq.gz -> 01_SE100_21CS500658TEST_1.fastq.gz
Concatenation file size check successful!
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500658TEST_2.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500658TEST_2.fastq.gz, HN33FDSXY_L1_01_SE100_21CS500658TEST_2.fastq.gz, HN33FDSXY_L2_01_SE100_21CS500658TEST_2.fastq.gz, HN33FDSXY_L3_01_SE100_21CS500658TEST_2.fastq.gz, HN33FDSXY_L4_01_SE100_21CS500658TEST_2.fastq.gz -> 01_SE100_21CS500658TEST_2.fastq.gz
Concatenation file size check successful!
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A3/2021-03-18/H3YY3DRXY_395698_S92_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500659TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A3/2021-03-18/H3YY3DRXY_395698_S92_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500659TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A3/2021-03-18/H3YY3DRXY_395698_S92_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500659TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A3/2021-03-18/H3YY3DRXY_395698_S92_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500659TEST_2.fastq.gz
Concatenation in progress for sample: ACC7703A3
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500659TEST_1.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500659TEST_1.fastq.gz -> 01_SE100_21CS500659TEST_1.fastq.gz
Concatenation file size check successful!
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500659TEST_2.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500659TEST_2.fastq.gz -> 01_SE100_21CS500659TEST_2.fastq.gz
Concatenation file size check successful!
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A4/2021-03-18/H3YY3DRXY_395698_S100_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500660TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A4/2021-03-18/H3YY3DRXY_395698_S100_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500660TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A4/2021-03-18/H3YY3DRXY_395698_S100_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500660TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A4/2021-03-18/H3YY3DRXY_395698_S100_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500660TEST_2.fastq.gz
Concatenation in progress for sample: ACC7703A4
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500660TEST_1.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500660TEST_1.fastq.gz -> 01_SE100_21CS500660TEST_1.fastq.gz
Concatenation file size check successful!
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500660TEST_2.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500660TEST_2.fastq.gz -> 01_SE100_21CS500660TEST_2.fastq.gz
Concatenation file size check successful!
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A5/2021-03-18/H3YY3DRXY_395698_S108_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500661TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A5/2021-03-18/H3YY3DRXY_395698_S108_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500661TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A5/2021-03-18/H3YY3DRXY_395698_S108_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500661TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A5/2021-03-18/H3YY3DRXY_395698_S108_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500661TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L1_01_SE100_21CS500661TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L1_01_SE100_21CS500661TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L2_01_SE100_21CS500661TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L2_01_SE100_21CS500661TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L003_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L3_01_SE100_21CS500661TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L003_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L3_01_SE100_21CS500661TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L004_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L4_01_SE100_21CS500661TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A5/2021-03-18/HN33FDSXY_395698_S9_L004_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L4_01_SE100_21CS500661TEST_2.fastq.gz
Concatenation in progress for sample: ACC7703A5
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500661TEST_1.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500661TEST_1.fastq.gz, HN33FDSXY_L1_01_SE100_21CS500661TEST_1.fastq.gz, HN33FDSXY_L2_01_SE100_21CS500661TEST_1.fastq.gz, HN33FDSXY_L3_01_SE100_21CS500661TEST_1.fastq.gz, HN33FDSXY_L4_01_SE100_21CS500661TEST_1.fastq.gz -> 01_SE100_21CS500661TEST_1.fastq.gz
Concatenation file size check successful!
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500661TEST_2.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500661TEST_2.fastq.gz, HN33FDSXY_L1_01_SE100_21CS500661TEST_2.fastq.gz, HN33FDSXY_L2_01_SE100_21CS500661TEST_2.fastq.gz, HN33FDSXY_L3_01_SE100_21CS500661TEST_2.fastq.gz, HN33FDSXY_L4_01_SE100_21CS500661TEST_2.fastq.gz -> 01_SE100_21CS500661TEST_2.fastq.gz
Concatenation file size check successful!
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A6/2021-03-18/H3YY3DRXY_395698_S115_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500662TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A6/2021-03-18/H3YY3DRXY_395698_S115_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500662TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A6/2021-03-18/H3YY3DRXY_395698_S115_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500662TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A6/2021-03-18/H3YY3DRXY_395698_S115_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500662TEST_2.fastq.gz
Concatenation in progress for sample: ACC7703A6
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500662TEST_1.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500662TEST_1.fastq.gz -> 01_SE100_21CS500662TEST_1.fastq.gz
Concatenation file size check successful!
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500662TEST_2.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500662TEST_2.fastq.gz -> 01_SE100_21CS500662TEST_2.fastq.gz
Concatenation file size check successful!
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A7/2021-03-18/H3YY3DRXY_395698_S122_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500663TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A7/2021-03-18/H3YY3DRXY_395698_S122_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500663TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A7/2021-03-18/H3YY3DRXY_395698_S122_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500663TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A7/2021-03-18/H3YY3DRXY_395698_S122_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500663TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L1_01_SE100_21CS500663TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L1_01_SE100_21CS500663TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L2_01_SE100_21CS500663TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L2_01_SE100_21CS500663TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L003_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L3_01_SE100_21CS500663TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L003_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L3_01_SE100_21CS500663TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L004_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L4_01_SE100_21CS500663TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A7/2021-03-18/HN33FDSXY_395698_S11_L004_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L4_01_SE100_21CS500663TEST_2.fastq.gz
Concatenation in progress for sample: ACC7703A7
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500663TEST_1.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500663TEST_1.fastq.gz, HN33FDSXY_L1_01_SE100_21CS500663TEST_1.fastq.gz, HN33FDSXY_L2_01_SE100_21CS500663TEST_1.fastq.gz, HN33FDSXY_L3_01_SE100_21CS500663TEST_1.fastq.gz, HN33FDSXY_L4_01_SE100_21CS500663TEST_1.fastq.gz -> 01_SE100_21CS500663TEST_1.fastq.gz
Concatenation file size check successful!
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500663TEST_2.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500663TEST_2.fastq.gz, HN33FDSXY_L1_01_SE100_21CS500663TEST_2.fastq.gz, HN33FDSXY_L2_01_SE100_21CS500663TEST_2.fastq.gz, HN33FDSXY_L3_01_SE100_21CS500663TEST_2.fastq.gz, HN33FDSXY_L4_01_SE100_21CS500663TEST_2.fastq.gz -> 01_SE100_21CS500663TEST_2.fastq.gz
Concatenation file size check successful!
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A8/2021-03-18/H3YY3DRXY_395698_S129_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500664TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A8/2021-03-18/H3YY3DRXY_395698_S129_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500664TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A8/2021-03-18/H3YY3DRXY_395698_S129_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500664TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A8/2021-03-18/H3YY3DRXY_395698_S129_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500664TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L1_01_SE100_21CS500664TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L1_01_SE100_21CS500664TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L2_01_SE100_21CS500664TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L2_01_SE100_21CS500664TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L003_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L3_01_SE100_21CS500664TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L003_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L3_01_SE100_21CS500664TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L004_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L4_01_SE100_21CS500664TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A8/2021-03-18/HN33FDSXY_395698_S12_L004_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L4_01_SE100_21CS500664TEST_2.fastq.gz
Concatenation in progress for sample: ACC7703A8
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500664TEST_1.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500664TEST_1.fastq.gz, HN33FDSXY_L1_01_SE100_21CS500664TEST_1.fastq.gz, HN33FDSXY_L2_01_SE100_21CS500664TEST_1.fastq.gz, HN33FDSXY_L3_01_SE100_21CS500664TEST_1.fastq.gz, HN33FDSXY_L4_01_SE100_21CS500664TEST_1.fastq.gz -> 01_SE100_21CS500664TEST_1.fastq.gz
Concatenation file size check successful!
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500664TEST_2.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500664TEST_2.fastq.gz, HN33FDSXY_L1_01_SE100_21CS500664TEST_2.fastq.gz, HN33FDSXY_L2_01_SE100_21CS500664TEST_2.fastq.gz, HN33FDSXY_L3_01_SE100_21CS500664TEST_2.fastq.gz, HN33FDSXY_L4_01_SE100_21CS500664TEST_2.fastq.gz -> 01_SE100_21CS500664TEST_2.fastq.gz
Concatenation file size check successful!
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A9/2021-03-18/H3YY3DRXY_395698_S77_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500665TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A9/2021-03-18/H3YY3DRXY_395698_S77_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500665TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A9/2021-03-18/H3YY3DRXY_395698_S77_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500665TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A9/2021-03-18/H3YY3DRXY_395698_S77_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500665TEST_2.fastq.gz
Concatenation in progress for sample: ACC7703A9
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500665TEST_1.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500665TEST_1.fastq.gz -> 01_SE100_21CS500665TEST_1.fastq.gz
Concatenation file size check successful!
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500665TEST_2.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500665TEST_2.fastq.gz -> 01_SE100_21CS500665TEST_2.fastq.gz
Concatenation file size check successful!
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A10/2021-03-18/H3YY3DRXY_395698_S85_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500666TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A10/2021-03-18/H3YY3DRXY_395698_S85_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500666TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A10/2021-03-18/H3YY3DRXY_395698_S85_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500666TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A10/2021-03-18/H3YY3DRXY_395698_S85_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500666TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L1_01_SE100_21CS500666TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L1_01_SE100_21CS500666TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L2_01_SE100_21CS500666TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L2_01_SE100_21CS500666TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L003_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L3_01_SE100_21CS500666TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L003_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L3_01_SE100_21CS500666TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L004_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L4_01_SE100_21CS500666TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A10/2021-03-18/HN33FDSXY_395698_S4_L004_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L4_01_SE100_21CS500666TEST_2.fastq.gz
Concatenation in progress for sample: ACC7703A10
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500666TEST_1.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500666TEST_1.fastq.gz, HN33FDSXY_L1_01_SE100_21CS500666TEST_1.fastq.gz, HN33FDSXY_L2_01_SE100_21CS500666TEST_1.fastq.gz, HN33FDSXY_L3_01_SE100_21CS500666TEST_1.fastq.gz, HN33FDSXY_L4_01_SE100_21CS500666TEST_1.fastq.gz -> 01_SE100_21CS500666TEST_1.fastq.gz
Concatenation file size check successful!
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500666TEST_2.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500666TEST_2.fastq.gz, HN33FDSXY_L1_01_SE100_21CS500666TEST_2.fastq.gz, HN33FDSXY_L2_01_SE100_21CS500666TEST_2.fastq.gz, HN33FDSXY_L3_01_SE100_21CS500666TEST_2.fastq.gz, HN33FDSXY_L4_01_SE100_21CS500666TEST_2.fastq.gz -> 01_SE100_21CS500666TEST_2.fastq.gz
Concatenation file size check successful!
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A11/2021-03-18/H3YY3DRXY_395698_S93_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500667TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A11/2021-03-18/H3YY3DRXY_395698_S93_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500667TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A11/2021-03-18/H3YY3DRXY_395698_S93_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500667TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A11/2021-03-18/H3YY3DRXY_395698_S93_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500667TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L1_01_SE100_21CS500667TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L1_01_SE100_21CS500667TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L2_01_SE100_21CS500667TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L2_01_SE100_21CS500667TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L003_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L3_01_SE100_21CS500667TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L003_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L3_01_SE100_21CS500667TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L004_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L4_01_SE100_21CS500667TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A11/2021-03-18/HN33FDSXY_395698_S6_L004_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/HN33FDSXY_L4_01_SE100_21CS500667TEST_2.fastq.gz
Concatenation in progress for sample: ACC7703A11
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500667TEST_1.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500667TEST_1.fastq.gz, HN33FDSXY_L1_01_SE100_21CS500667TEST_1.fastq.gz, HN33FDSXY_L2_01_SE100_21CS500667TEST_1.fastq.gz, HN33FDSXY_L3_01_SE100_21CS500667TEST_1.fastq.gz, HN33FDSXY_L4_01_SE100_21CS500667TEST_1.fastq.gz -> 01_SE100_21CS500667TEST_1.fastq.gz
Concatenation file size check successful!
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500667TEST_2.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500667TEST_2.fastq.gz, HN33FDSXY_L1_01_SE100_21CS500667TEST_2.fastq.gz, HN33FDSXY_L2_01_SE100_21CS500667TEST_2.fastq.gz, HN33FDSXY_L3_01_SE100_21CS500667TEST_2.fastq.gz, HN33FDSXY_L4_01_SE100_21CS500667TEST_2.fastq.gz -> 01_SE100_21CS500667TEST_2.fastq.gz
Concatenation file size check successful!
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A12/2021-03-18/H3YY3DRXY_395698_S101_L001_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500668TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A12/2021-03-18/H3YY3DRXY_395698_S101_L001_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L1_01_SE100_21CS500668TEST_2.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A12/2021-03-18/H3YY3DRXY_395698_S101_L002_R1_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500668TEST_1.fastq.gz
Linking: /home/proj/stage/housekeeper-bundles/ACC7703A12/2021-03-18/H3YY3DRXY_395698_S101_L002_R2_001.fastq.gz -> /home/proj/stage/mutant/cases/frankhusky/fastq/H3YY3DRXY_L2_01_SE100_21CS500668TEST_2.fastq.gz
Concatenation in progress for sample: ACC7703A12
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500668TEST_1.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500668TEST_1.fastq.gz -> 01_SE100_21CS500668TEST_1.fastq.gz
Concatenation file size check successful!
Concatenating: H3YY3DRXY_L1_01_SE100_21CS500668TEST_2.fastq.gz, H3YY3DRXY_L2_01_SE100_21CS500668TEST_2.fastq.gz -> 01_SE100_21CS500668TEST_2.fastq.gz
Concatenation file size check successful!
Saved config to /home/proj/stage/mutant/cases/frankhusky/case_config.json
Action running set for case frankhusky
Running command /home/proj/stage/bin/miniconda3/bin/conda run --name S_mutant /home/proj/stage/bin/miniconda3/envs/S_mutant/bin/mutant analyse sarscov2 --config_case /home/proj/stage/mutant/cases/frankhusky/case_config.json --outdir /home/proj/stage/mutant/cases/frankhusky/results /home/proj/stage/mutant/cases/frankhusky/fastq
Case frankhusky exists in Status DB
Storing bundle data in Housekeeper for frankhusky
Converting pipeline deliverables to CG deliverables
Running command /home/proj/stage/bin/miniconda3/envs/S_hermes/bin/hermes convert deliverables --pipeline mutant /home/proj/stage/mutant/cases/frankhusky/results/frankhusky_deliverables.yaml
Use global root path /home/proj/stage/housekeeper-bundles
created new bundle version dir: /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19
linked file: /home/proj/stage/mutant/cases/frankhusky/results/instrument.properties -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/instrument.properties
linked file: /home/proj/stage/mutant/cases/frankhusky/results/sars-cov-2_395698_results.csv -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/sars-cov-2_395698_results.csv
linked file: /home/proj/stage/mutant/cases/frankhusky/results/sars-cov-2_395698_variants.csv -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/sars-cov-2_395698_variants.csv
linked file: /home/proj/stage/mutant/cases/frankhusky/results/395698.pangolin.csv -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698.pangolin.csv
linked file: /home/proj/stage/mutant/cases/frankhusky/results/395698_2024-01-19_pangolin_classification_format4.txt -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698_2024-01-19_pangolin_classification_format4.txt
linked file: /home/proj/stage/mutant/cases/frankhusky/results/395698.consensus.fa -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698.consensus.fa
linked file: /home/proj/stage/mutant/cases/frankhusky/results/395698_multiqc.html -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698_multiqc.html
linked file: /home/proj/stage/mutant/cases/frankhusky/results/395698_multiqc.json -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698_multiqc.json
linked file: /home/proj/stage/mutant/cases/frankhusky/results/nextclade_summary.csv -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/nextclade_summary.csv
linked file: /home/proj/stage/mutant/cases/frankhusky/results/frankhusky_metrics_deliverables.yaml -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/frankhusky_metrics_deliverables.yaml
linked file: /home/proj/stage/mutant/cases/frankhusky/case_config.json -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/case_config.json
linked file: /home/proj/stage/mutant/MUTANT/mutant/config/hasta/illumina_artic_v3.json -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/illumina_artic_v3.json
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_versions/frankhusky_240119-152718_versions.csv -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/frankhusky_240119-152718_versions.csv
linked file: /home/proj/stage/mutant/cases/frankhusky/results/nextflow.log -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/nextflow.log
linked file: /home/proj/stage/mutant/cases/frankhusky/results/395698_komplettering.csv -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698_komplettering.csv
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500657TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500657TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500657TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500657TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500657TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500657TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500657TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500657TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500658TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500658TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500658TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500658TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500658TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500658TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500658TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500658TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500659TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500659TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500659TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500659TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500659TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500659TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500659TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500659TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500660TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500660TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500660TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500660TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500660TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500660TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500660TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500660TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500661TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500661TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500661TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500661TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500661TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500661TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500661TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500661TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500662TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500662TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500662TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500662TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500662TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500662TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500662TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500662TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500663TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500663TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500663TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500663TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500663TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500663TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500663TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500663TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500664TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500664TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500664TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500664TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500664TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500664TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500664TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500664TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500665TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500665TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500665TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500665TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500665TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500665TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500665TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500665TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500666TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500666TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500666TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500666TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500666TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500666TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500666TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500666TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500667TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500667TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500667TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500667TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500667TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500667TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500667TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500667TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500668TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500668TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500668TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500668TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500668TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500668TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500668TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500668TEST.consensus.fasta
/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/apps/housekeeper/hk.py:328: SAWarning: Object of type <Version> not in session, add operation along 'Bundle.versions' will not proceed
  return self._store.session.commit()
/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/apps/housekeeper/hk.py:328: SAWarning: Object of type <File> not in session, add operation along 'Tag.files' won't proceed
  return self._store.session.commit()
Analysis successfully stored in Housekeeper: frankhusky : 2024-01-19 15:45:09
Storing analysis in StatusDB for frankhusky
Running command /home/proj/stage/bin/miniconda3/bin/conda run --name S_mutant /home/proj/stage/bin/miniconda3/envs/S_mutant/bin/mutant --version
Analysis successfully stored in StatusDB: frankhusky : 2024-01-19 15:45:09
Action None set for case frankhusky
Screenshot 2024-01-19 at 15 35 35 
[henrik.stranneheim@hasta:~] [S_base] $ housekeeper get bundle -v frankhusky
2024-01-19 15:50:56 hasta.scilifelab.se housekeeper.cli.core[197006] INFO Use root path /home/proj/stage/housekeeper-bundles
                        πŸ“¦ Bundle table πŸ“¦
┏━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓
┃ ID    ┃ Bundle name ┃ Version IDs                  ┃ Created    ┃
┑━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩
β”‚ 34813 β”‚ frankhusky  β”‚ 172054, 119221, 45832, 36671 β”‚ 2021-04-21 β”‚
β””β”€β”€β”€β”€β”€β”€β”€β”΄β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”΄β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”΄β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”˜
                               πŸ“• Version table πŸ“•
┏━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━┓
┃ ID     ┃ Bundle name ┃ Nr files ┃ Included   ┃ Archived ┃ Created    ┃ Expires ┃
┑━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━┩
β”‚ 172054 β”‚ frankhusky  β”‚ 63       β”‚ 2024-01-19 β”‚          β”‚ 2024-01-19 β”‚         β”‚
β””β”€β”€β”€β”€β”€β”€β”€β”€β”΄β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”΄β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”΄β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”΄β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”΄β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”΄β”€β”€β”€β”€β”€β”€β”€β”€β”€β”˜
                                                                                  πŸ“œ Files table πŸ“œ
┏━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ ID      ┃ File name                                                                           ┃ Tags                                                                               ┃
┑━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
β”‚ 5271017 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/instrument.properties    β”‚ storage, frankhusky, fohm-delivery, instrument-properties                          β”‚
β”‚ 5271018 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/sars-cov-2_395698_resul… β”‚ deliver, visualization, typing-report, csv, frankhusky, ks-delivery, ks-results    β”‚
β”‚ 5271019 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/sars-cov-2_395698_varia… β”‚ deliver, visualization, typing-report, csv, frankhusky, ks-delivery,               β”‚
β”‚         β”‚                                                                                     β”‚ ks-aux-results                                                                     β”‚
β”‚ 5271020 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698.pangolin.csv      β”‚ visualization, csv, frankhusky, fohm-delivery, pangolin-typing                     β”‚
β”‚ 5271021 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698_2024-01-19_pango… β”‚ deliver, csv, frankhusky, fohm-delivery, pangolin-typing-fohm                      β”‚
β”‚ 5271022 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698.consensus.fa      β”‚ fastq, deliver, storage, consensus, frankhusky, ks-delivery                        β”‚
β”‚ 5271023 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698_multiqc.html      β”‚ multiqc-html, deliver, frankhusky, ks-delivery                                     β”‚
β”‚ 5271024 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698_multiqc.json      β”‚ multiqc-json, vogue, frankhusky                                                    β”‚
β”‚ 5271025 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/nextclade_summary.csv    β”‚ deliver, frankhusky, ks-delivery, typing-summary, nextclade                        β”‚
β”‚ 5271026 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/frankhusky_metrics_deli… β”‚ metrics, vogue, frankhusky                                                         β”‚
β”‚ 5271027 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/case_config.json         β”‚ config, storage, frankhusky                                                        β”‚
β”‚ 5271028 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/illumina_artic_v3.json   β”‚ storage, mutant-config, frankhusky                                                 β”‚
β”‚ 5271029 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/frankhusky_240119-15271… β”‚ storage, frankhusky, software-versions                                             β”‚
β”‚ 5271030 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/nextflow.log             β”‚ mutant-log, frankhusky                                                             β”‚
β”‚ 5271031 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698_komplettering.csv β”‚ deliver, visualization, komplettering, frankhusky, fohm-delivery                   β”‚
β”‚ 5271032 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500657TEST… β”‚ fastq, storage, forward-strand, ACC7703A1                                          β”‚
β”‚ 5271033 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500657TEST… β”‚ fastq, storage, reverse-strand, ACC7703A1                                          β”‚
β”‚ 5271034 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500657TEST… β”‚ vcf, deliver, vcf-report, ACC7703A1, fohm-delivery                                 β”‚
β”‚ 5271035 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500657TEST… β”‚ deliver, storage, ACC7703A1, fohm-delivery, fasta, consensus-sample                β”‚
β”‚ 5271036 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500658TEST… β”‚ fastq, storage, forward-strand, ACC7703A2                                          β”‚
β”‚ 5271037 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500658TEST… β”‚ fastq, storage, reverse-strand, ACC7703A2                                          β”‚
β”‚ 5271038 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500658TEST… β”‚ vcf, deliver, vcf-report, ACC7703A2, fohm-delivery                                 β”‚
β”‚ 5271039 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500658TEST… β”‚ deliver, storage, ACC7703A2, fohm-delivery, fasta, consensus-sample                β”‚
β”‚ 5271040 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500659TEST… β”‚ fastq, storage, forward-strand, ACC7703A3                                          β”‚
β”‚ 5271041 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500659TEST… β”‚ fastq, storage, reverse-strand, ACC7703A3                                          β”‚
β”‚ 5271042 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500659TEST… β”‚ vcf, deliver, vcf-report, ACC7703A3, fohm-delivery                                 β”‚
β”‚ 5271043 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500659TEST… β”‚ deliver, storage, ACC7703A3, fohm-delivery, fasta, consensus-sample                β”‚
β”‚ 5271044 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500660TEST… β”‚ fastq, storage, forward-strand, ACC7703A4                                          β”‚
β”‚ 5271045 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500660TEST… β”‚ fastq, storage, reverse-strand, ACC7703A4                                          β”‚
β”‚ 5271046 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500660TEST… β”‚ vcf, deliver, vcf-report, ACC7703A4, fohm-delivery                                 β”‚
β”‚ 5271047 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500660TEST… β”‚ deliver, storage, ACC7703A4, fohm-delivery, fasta, consensus-sample                β”‚
β”‚ 5271048 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500661TEST… β”‚ fastq, storage, forward-strand, ACC7703A5                                          β”‚
β”‚ 5271049 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500661TEST… β”‚ fastq, storage, reverse-strand, ACC7703A5                                          β”‚
β”‚ 5271050 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500661TEST… β”‚ vcf, deliver, vcf-report, ACC7703A5, fohm-delivery                                 β”‚
β”‚ 5271051 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500661TEST… β”‚ deliver, storage, ACC7703A5, fohm-delivery, fasta, consensus-sample                β”‚
β”‚ 5271052 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500662TEST… β”‚ fastq, storage, forward-strand, ACC7703A6                                          β”‚
β”‚ 5271053 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500662TEST… β”‚ fastq, storage, reverse-strand, ACC7703A6                                          β”‚
β”‚ 5271054 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500662TEST… β”‚ vcf, deliver, vcf-report, ACC7703A6, fohm-delivery                                 β”‚
β”‚ 5271055 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500662TEST… β”‚ deliver, storage, ACC7703A6, fohm-delivery, fasta, consensus-sample                β”‚
β”‚ 5271056 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500663TEST… β”‚ fastq, storage, forward-strand, ACC7703A7                                          β”‚
β”‚ 5271057 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500663TEST… β”‚ fastq, storage, reverse-strand, ACC7703A7                                          β”‚
β”‚ 5271058 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500663TEST… β”‚ vcf, deliver, vcf-report, ACC7703A7, fohm-delivery                                 β”‚
β”‚ 5271059 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500663TEST… β”‚ deliver, storage, ACC7703A7, fohm-delivery, fasta, consensus-sample                β”‚
β”‚ 5271060 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500664TEST… β”‚ fastq, storage, forward-strand, ACC7703A8                                          β”‚
β”‚ 5271061 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500664TEST… β”‚ fastq, storage, reverse-strand, ACC7703A8                                          β”‚
β”‚ 5271062 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500664TEST… β”‚ vcf, deliver, vcf-report, ACC7703A8, fohm-delivery                                 β”‚
β”‚ 5271063 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500664TEST… β”‚ deliver, storage, ACC7703A8, fohm-delivery, fasta, consensus-sample                β”‚
β”‚ 5271064 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500665TEST… β”‚ fastq, storage, forward-strand, ACC7703A9                                          β”‚
β”‚ 5271065 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500665TEST… β”‚ fastq, storage, reverse-strand, ACC7703A9                                          β”‚
β”‚ 5271066 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500665TEST… β”‚ vcf, deliver, vcf-report, ACC7703A9, fohm-delivery                                 β”‚
β”‚ 5271067 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500665TEST… β”‚ deliver, storage, ACC7703A9, fohm-delivery, fasta, consensus-sample                β”‚
β”‚ 5271068 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500666TEST… β”‚ fastq, storage, forward-strand, ACC7703A10                                         β”‚
β”‚ 5271069 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500666TEST… β”‚ fastq, storage, reverse-strand, ACC7703A10                                         β”‚
β”‚ 5271070 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500666TEST… β”‚ vcf, deliver, vcf-report, ACC7703A10, fohm-delivery                                β”‚
β”‚ 5271071 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500666TEST… β”‚ deliver, storage, ACC7703A10, fohm-delivery, fasta, consensus-sample               β”‚
β”‚ 5271072 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500667TEST… β”‚ fastq, storage, forward-strand, ACC7703A11                                         β”‚
β”‚ 5271073 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500667TEST… β”‚ fastq, storage, reverse-strand, ACC7703A11                                         β”‚
β”‚ 5271074 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500667TEST… β”‚ vcf, deliver, vcf-report, ACC7703A11, fohm-delivery                                β”‚
β”‚ 5271075 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500667TEST… β”‚ deliver, storage, ACC7703A11, fohm-delivery, fasta, consensus-sample               β”‚
β”‚ 5271076 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500668TEST… β”‚ fastq, storage, forward-strand, ACC7703A12                                         β”‚
β”‚ 5271077 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500668TEST… β”‚ fastq, storage, reverse-strand, ACC7703A12                                         β”‚
β”‚ 5271078 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500668TEST… β”‚ vcf, deliver, vcf-report, ACC7703A12, fohm-delivery                                β”‚
β”‚ 5271079 β”‚ /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500668TEST… β”‚ deliver, storage, ACC7703A12, fohm-delivery, fasta, consensus-sample               β”‚
β””β”€β”€β”€β”€β”€β”€β”€β”€β”€β”΄β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”΄β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”˜
Screenshot 2024-01-19 at 15 54 41
islean commented 8 months ago

I don't really like doing data migration via Alembic, and I think we should reserve ourselves to doing architectural changes. Would be good to document data migrations somehow, though. Any thoughts @Clinical-Genomics/sysdev ? Do you prefer it being an alembic script or do you have other ideas?

Might be fine here though, there is no real risk involved that I can think of.

ChrOertlin commented 8 months ago

Might be fine here though, there is no real risk involved that I can think of.

I think here it is ok as it is just changing a string to a different one. I think it gets tricky when data gets deleted etc.

sonarcloud[bot] commented 8 months ago

Quality Gate Passed Quality Gate passed

Kudos, no new issues were introduced!

0 New issues
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

henrikstranneheim commented 8 months ago

Failed Alembic migration when deployind:

20.2.5     -> 20.2.5
Already on 'master'
Your branch is behind 'origin/master' by 2 commits, and can be fast-forwarded.
  (use "git pull" to update your local branch)
Updating c660742..a39a383
Fast-forward
 .bumpversion.cfg                                                        |  2 +-
 alembic/versions/2024_01_19_bebe0db0c8de_rename_sars_cov_2_to_mutant.py | 41 +++++++++++++++++++++++++++++++++++++++++
 setup.py                                                                |  2 +-
 3 files changed, 43 insertions(+), 2 deletions(-)
 create mode 100644 alembic/versions/2024_01_19_bebe0db0c8de_rename_sars_cov_2_to_mutant.py
/home/henrik.stranneheim
INFO  [alembic.runtime.migration] Context impl MySQLImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.
ERROR [alembic.util.messaging] Multiple head revisions are present for given argument 'head'; please specify a specific target revision, '<branchname>@head' to narrow to a specific head, or 'heads' for all heads
  FAILED: Multiple head revisions are present for given argument 'head'; please specify a specific target revision, '<branchname>@head' to narrow to a specific head, or 'heads' for all
  heads
ΞΈ64Β° [henrik.stranneheim@hasta:~] [P_base] 1m30s 255 $

Fixed here: https://github.com/Clinical-Genomics/trailblazer/pull/375