_source activate S_microSALT_
Remove all result folders for MIC3109 and MIC4109 /home/proj/stage/microbial/results.
microSALT analyse project MIC3109
microSALT utils autobatch --dry
Verify that the autobatch command outputs correct output
microSALT utils autobatch
microSALT utils autobatch --dry
Verify that the autobatch command outputs correct output
microSALT utils autobatch
Verify that no project is started this time.
_Verify that the results for projects MIC3109 & MIC4109 are consistent with the results attached to AMSystem doc 1490, MicrobialWGS.xlsx
Test results
These are the results of the tests, and necessary conclusions, that prove the stability of the PR.
Tests resolved as expected. For details regarding autobatch specific output, see below:
14:17:53 ~> microSALT analyse project MIC3109
INFO - Verifying LIMS connection...
INFO - Checking versions of references..
WARNING - Unable to find requested organism 'Unset' in pubMLST database
INFO - Cached resFinder database identical to remote.
INFO - Re-indexed contents of /home/proj/bin/conda/envs/S_microSALT/expec
INFO - Version check done. Creating sbatch jobs
WARNING - Record [CG_ID_project]=[MIC3109] in table Projects already exists
INFO - Created runfile for sample MIC3109A3 in folder /home/proj/stage/microbial/results//MIC3109_2020.2.5_14.18.19/MIC3109A3
WARNING - Record [CG_ID_sample]=[MIC3109A3] in table Samples already exists
INFO - Created runfile for sample MIC3109A2 in folder /home/proj/stage/microbial/results//MIC3109_2020.2.5_14.18.19/MIC3109A2
WARNING - Record [CG_ID_sample]=[MIC3109A2] in table Samples already exists
INFO - Created runfile for sample MIC3109A4 in folder /home/proj/stage/microbial/results//MIC3109_2020.2.5_14.18.19/MIC3109A4
WARNING - Record [CG_ID_sample]=[MIC3109A4] in table Samples already exists
INFO - Created runfile for sample MIC3109A5 in folder /home/proj/stage/microbial/results//MIC3109_2020.2.5_14.18.19/MIC3109A5
WARNING - Record [CG_ID_sample]=[MIC3109A5] in table Samples already exists
INFO - Created runfile for sample MIC3109A1 in folder /home/proj/stage/microbial/results//MIC3109_2020.2.5_14.18.19/MIC3109A1
WARNING - Record [CG_ID_sample]=[MIC3109A1] in table Samples already exists
INFO - Execution finished!
14:19:11 ~> microSALT utils autobatch --dry
INFO - Verifying LIMS connection...
INFO - Cached resFinder database identical to remote.
INFO - Skipping ACC5466 due to concurrent SLURM run
INFO - Skipping MIC3557 due to existing analysis in results folder
INFO - Skipping ACC5702 due to existing analysis in results folder
INFO - Skipping ACC5710 due to existing analysis in results folder
INFO - Skipping ACC6438 due to existing analysis in results folder
INFO - Skipping ACC5955 due to existing analysis in results folder
INFO - Skipping ACC5551 due to existing analysis in results folder
INFO - Skipping MIC3552 due to existing analysis in results folder
INFO - Skipping MIC4107 due to existing analysis in results folder
DRY - microSALT analyse MIC4109 --skip_update
INFO - Skipping MIC3109 due to concurrent SLURM run
14:19:28 ~> microSALT utils autobatch
INFO - Verifying LIMS connection...
INFO - Cached resFinder database identical to remote.
INFO - Verifying LIMS connection...
WARNING - Record [CG_ID_project]=[MIC4109] in table Projects already exists
INFO - Created runfile for sample MIC4109A22 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A22
WARNING - Record [CG_ID_sample]=[MIC4109A22] in table Samples already exists
INFO - Created runfile for sample MIC4109A21 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A21
WARNING - Record [CG_ID_sample]=[MIC4109A21] in table Samples already exists
INFO - Created runfile for sample MIC4109A9 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A9
WARNING - Record [CG_ID_sample]=[MIC4109A9] in table Samples already exists
INFO - Created runfile for sample MIC4109A17 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A17
WARNING - Record [CG_ID_sample]=[MIC4109A17] in table Samples already exists
INFO - Created runfile for sample MIC4109A14 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A14
WARNING - Record [CG_ID_sample]=[MIC4109A14] in table Samples already exists
INFO - Created runfile for sample MIC4109A24 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A24
WARNING - Record [CG_ID_sample]=[MIC4109A24] in table Samples already exists
INFO - Created runfile for sample MIC4109A19 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A19
WARNING - Record [CG_ID_sample]=[MIC4109A19] in table Samples already exists
INFO - Created runfile for sample MIC4109A13 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A13
WARNING - Record [CG_ID_sample]=[MIC4109A13] in table Samples already exists
INFO - Created runfile for sample MIC4109A10 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A10
WARNING - Record [CG_ID_sample]=[MIC4109A10] in table Samples already exists
INFO - Created runfile for sample MIC4109A23 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A23
WARNING - Record [CG_ID_sample]=[MIC4109A23] in table Samples already exists
INFO - Created runfile for sample MIC4109A16 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A16
WARNING - Record [CG_ID_sample]=[MIC4109A16] in table Samples already exists
INFO - Created runfile for sample MIC4109A15 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A15
WARNING - Record [CG_ID_sample]=[MIC4109A15] in table Samples already exists
INFO - Created runfile for sample MIC4109A18 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A18
WARNING - Record [CG_ID_sample]=[MIC4109A18] in table Samples already exists
INFO - Created runfile for sample MIC4109A26 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A26
WARNING - Record [CG_ID_sample]=[MIC4109A26] in table Samples already exists
INFO - Created runfile for sample MIC4109A1 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A1
WARNING - Record [CG_ID_sample]=[MIC4109A1] in table Samples already exists
INFO - Created runfile for sample MIC4109A25 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A25
WARNING - Record [CG_ID_sample]=[MIC4109A25] in table Samples already exists
INFO - Created runfile for sample MIC4109A3 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A3
WARNING - Record [CG_ID_sample]=[MIC4109A3] in table Samples already exists
INFO - Created runfile for sample MIC4109A2 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A2
WARNING - Record [CG_ID_sample]=[MIC4109A2] in table Samples already exists
INFO - Created runfile for sample MIC4109A20 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A20
WARNING - Record [CG_ID_sample]=[MIC4109A20] in table Samples already exists
INFO - Created runfile for sample MIC4109A7 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A7
WARNING - Record [CG_ID_sample]=[MIC4109A7] in table Samples already exists
INFO - Created runfile for sample MIC4109A6 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A6
WARNING - Record [CG_ID_sample]=[MIC4109A6] in table Samples already exists
INFO - Created runfile for sample MIC4109A11 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A11
WARNING - Record [CG_ID_sample]=[MIC4109A11] in table Samples already exists
INFO - Created runfile for sample MIC4109A12 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A12
WARNING - Record [CG_ID_sample]=[MIC4109A12] in table Samples already exists
INFO - Created runfile for sample MIC4109A8 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A8
WARNING - Record [CG_ID_sample]=[MIC4109A8] in table Samples already exists
INFO - Created runfile for sample MIC4109A5 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A5
WARNING - Record [CG_ID_sample]=[MIC4109A5] in table Samples already exists
INFO - Created runfile for sample MIC4109A4 in folder /home/proj/stage/microbial/results//MIC4109_2020.2.5_14.19.49/MIC4109A4
WARNING - Record [CG_ID_sample]=[MIC4109A4] in table Samples already exists
14:26:52 ~> microSALT utils autobatch --dry
INFO - Verifying LIMS connection...
INFO - Cached resFinder database identical to remote.
INFO - Skipping ACC5466 due to concurrent SLURM run
INFO - Skipping MIC3557 due to existing analysis in results folder
INFO - Skipping ACC5702 due to existing analysis in results folder
INFO - Skipping ACC5710 due to existing analysis in results folder
INFO - Skipping ACC6438 due to existing analysis in results folder
INFO - Skipping ACC5955 due to existing analysis in results folder
INFO - Skipping ACC5551 due to existing analysis in results folder
INFO - Skipping MIC3552 due to existing analysis in results folder
INFO - Skipping MIC4107 due to existing analysis in results folder
INFO - Skipping MIC4109 due to concurrent SLURM run
INFO - Skipping MIC3109 due to concurrent SLURM run
14:27:26 ~> microSALT utils autobatch
INFO - Verifying LIMS connection...
INFO - Cached resFinder database identical to remote.
MIC3109 and MIC4109 QC and Typing reports were reviewed. The QC report had a sub 5% difference compared to AMSystem doc 1490, Microbial_WGS.xlsx. The Typing report was identical.
Sign-offs
[X] Code reviewed by @patrikgrenfeldt
[X] Code tested by @sylvinite
[X] Approved to run at Clinical-Genomics by @patrikgrenfeldt
Description
The features of this PR primarily concerns bioinformaticians
It adds the utility command "autobatch" which checks the default input folder for new projects, and starts analysis for them.
Primary function of PR
Testing
This is a description of the tests necessary to verify the stability of the PR.
Basic test routine:
bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh autobatchussource activate S_microSALT_ Remove all result folders for MIC3109 and MIC4109/home/proj/stage/microbial/results.microSALT analyse project MIC3109microSALT utils autobatch --dryVerify that the autobatch command outputs correct outputmicroSALT utils autobatchmicroSALT utils autobatch --dryVerify that the autobatch command outputs correct outputmicroSALT utils autobatchVerify that no project is started this time._Verify that the results for projects MIC3109 & MIC4109 are consistent with the results attached to AMSystem doc 1490, MicrobialWGS.xlsx
Test results
These are the results of the tests, and necessary conclusions, that prove the stability of the PR. Tests resolved as expected. For details regarding autobatch specific output, see below:
MIC3109 and MIC4109 QC and Typing reports were reviewed. The QC report had a sub 5% difference compared to AMSystem doc 1490, Microbial_WGS.xlsx. The Typing report was identical.
Sign-offs