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Clinical-Genomics / demultiplexing

To keep scripts associated with execution of the Illumina demultiplexing pipeline
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Fix config files for demultiplexing #169

Closed beatrizsavinhas closed 1 year ago

beatrizsavinhas commented 1 year ago

This PR adds/fixes:

How to prepare for test:

How to test:

Expected test outcome:

Review:

This version is a:

beatrizsavinhas commented 1 year ago

Copied flowcell to stage

rsync -rvL /home/proj/production/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY/ /home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY/

Testing demultiplexing with master

θ63° 9d [hiseq.clinical@hasta:~] [S_base] 127 $ bash /home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.bash /home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY
[20230322093736] demuxtiles.bash VERSION 5.5.0
ERROR conda.cli.main_run:execute(41): `conda run /home/proj/stage/bin/miniconda3/envs/S_demux/bin//demux sheet validate --application wgs /home/proj/production/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY/SampleSheet.csv` failed. (See above for error)
Traceback (most recent call last):
  File "/home/proj/stage/bin/miniconda3/envs/S_demux/bin//demux", line 8, in <module>
    sys.exit(main())
  File "/home/proj/production/bin/git/cgstats/src/demux/demux/__main__.py", line 13, in main
    sys.exit(demux())
  File "/home/proj/stage/bin/miniconda3/envs/S_demux/lib/python3.7/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/proj/stage/bin/miniconda3/envs/S_demux/lib/python3.7/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/proj/stage/bin/miniconda3/envs/S_demux/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/proj/stage/bin/miniconda3/envs/S_demux/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/proj/stage/bin/miniconda3/envs/S_demux/lib/python3.7/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/proj/stage/bin/miniconda3/envs/S_demux/lib/python3.7/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/home/proj/production/bin/git/cgstats/src/demux/demux/cli/samplesheet.py", line 49, in validate
    HiSeqXSamplesheet(samplesheet).validate()
  File "/home/proj/production/bin/git/cgstats/src/demux/demux/utils/samplesheet.py", line 105, in __init__
    self.parse(samplesheet_path)
  File "/home/proj/production/bin/git/cgstats/src/demux/demux/utils/samplesheet.py", line 150, in parse
    raise SampleSheetParseException("No data found!")
demux.utils.samplesheet.SampleSheetParseException: No data found!

ls: cannot access /home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//projectlog.*.log: No such file or directory

Installing branch on stage

θ66° 9d [hiseq.clinical@hasta:~] [S_base] 46s 1 $ up
θ69° 10d [hiseq.clinical@hasta:~] [P_base] $ bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-demux-stage.sh fixing-demux-config-file
on the host hasta.scilifelab.se, continue
Collecting git+https://github.com/clinical-genomics/demultiplexing@fixing-demux-config-file
  Cloning https://github.com/clinical-genomics/demultiplexing (to revision fixing-demux-config-file) to ./tmp/pip-req-build-78rbxd7a
  Running command git clone --quiet https://github.com/clinical-genomics/demultiplexing /home/hiseq.clinical/tmp/pip-req-build-78rbxd7a
  Running command git checkout -b fixing-demux-config-file --track origin/fixing-demux-config-file
  Switched to a new branch 'fixing-demux-config-file'
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  Resolved https://github.com/clinical-genomics/demultiplexing to commit c822a89fc2901d0ea4a40783be7eddf258b5064c
  Installing build dependencies ... done
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Building wheels for collected packages: demux
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Collecting git+https://github.com/clinical-genomics/demultiplexing@fixing-demux-config-file
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Requirement already satisfied: MarkupSafe>=0.23 in /home/proj/stage/bin/miniconda3/envs/S_base/lib/python3.11/site-packages (from Jinja2<3.0,>=2.10.1->Flask>=1.1.1->cgstats==1.8.1) (2.0.1)
Requirement already satisfied: soupsieve>1.2 in /home/proj/stage/bin/miniconda3/envs/S_base/lib/python3.11/site-packages (from beautifulsoup4->bs4->cgstats==1.8.1) (2.4)
Building wheels for collected packages: cgstats, Flask-Bootstrap, git-lint, html-linter, docopt, template-remover, visitor
  Building wheel for cgstats (setup.py) ... done
  Created wheel for cgstats: filename=cgstats-1.8.1-py3-none-any.whl size=41298 sha256=9d5093e96d227c9a8a121b3350e6c5117260d989ec229ddecbd5078d7e922138
  Stored in directory: /home/hiseq.clinical/tmp/pip-ephem-wheel-cache-43sl34nt/wheels/1e/bb/51/7af8fb031f6b557c730656f70401b8acc92e0d1e6dc7ba74b5
  Building wheel for Flask-Bootstrap (setup.py) ... done
  Created wheel for Flask-Bootstrap: filename=Flask_Bootstrap-3.3.7.1-py3-none-any.whl size=460122 sha256=431b1ac336f8adbc8c448da1ea9cc6a979c72bcf3f3dce679a2dfbcd86d5b87d
  Stored in directory: /home/hiseq.clinical/.cache/pip/wheels/3a/a2/90/8d658b1e875f36bdad71cdece9598b08c465d44bea13b9f74c
  Building wheel for git-lint (setup.py) ... done
  Created wheel for git-lint: filename=git_lint-0.1.2-py3-none-any.whl size=38947 sha256=0428c8b7a87545e58cf5d2138753b661b7e1b7a3e9b8b17fa270382e168a4541
  Stored in directory: /home/hiseq.clinical/.cache/pip/wheels/3b/4e/58/dc0b85f91377644fcd08937805760defd69ecec466f87ebdee
  Building wheel for html-linter (setup.py) ... done
  Created wheel for html-linter: filename=html_linter-0.4.0-py3-none-any.whl size=14320 sha256=49a1999ba0f64a6709ef81c74b5232ea3cc43a9095fc70b58b43b134ca703df6
  Stored in directory: /home/hiseq.clinical/.cache/pip/wheels/e2/8a/b0/6bb76f8e8b2c6a9ea19cd5f75fd68edc88bbf7597ceaf6be58
  Building wheel for docopt (setup.py) ... done
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=7451103bfe6870d05f8235cbd06a68949996182ecec2c6e3e950c75285bd21ed
  Stored in directory: /home/hiseq.clinical/.cache/pip/wheels/1a/b0/8c/4b75c4116c31f83c8f9f047231251e13cc74481cca4a78a9ce
  Building wheel for template-remover (setup.py) ... done
  Created wheel for template-remover: filename=template_remover-0.1.9-py3-none-any.whl size=7026 sha256=98743a21deda60aa22ae9c6b41fc2d7010bc8c7926ca2d251f50531ac73a92bf
  Stored in directory: /home/hiseq.clinical/.cache/pip/wheels/f2/25/ae/4b864e7b86545282775c674fc3311748bcdb9b2cbb6013834a
  Building wheel for visitor (setup.py) ... done
  Created wheel for visitor: filename=visitor-0.1.3-py3-none-any.whl size=3926 sha256=19963ba13b68dde522fe05bae2d2d249d5e8ded6001addc73c080c9c66e1a772
  Stored in directory: /home/hiseq.clinical/.cache/pip/wheels/a6/7c/bb/66bee1b6af18bb643ec4e26a58e932c6373849f1f1918592fd
Successfully built cgstats Flask-Bootstrap git-lint html-linter docopt template-remover visitor
Installing collected packages: visitor, docopt, wrapt, tomlkit, template-remover, pycodestyle, platformdirs, pathspec, pathlib2, mccabe, lazy-object-proxy, isort, dominate, docutils, dill, bump2version, yamllint, html-linter, bumpversion, astroid, pylint, git-lint, Flask-Bootstrap, cgstats
Successfully installed Flask-Bootstrap-3.3.7.1 astroid-2.15.0 bump2version-1.0.1 bumpversion-0.6.0 cgstats-1.8.1 dill-0.3.6 docopt-0.6.2 docutils-0.19 dominate-2.7.0 git-lint-0.1.2 html-linter-0.4.0 isort-5.12.0 lazy-object-proxy-1.9.0 mccabe-0.7.0 pathlib2-2.3.7.post1 pathspec-0.11.1 platformdirs-3.1.1 pycodestyle-2.10.0 pylint-2.17.0 template-remover-0.1.9 tomlkit-0.11.6 visitor-0.1.3 wrapt-1.15.0 yamllint-1.29.0
remote: Enumerating objects: 49, done.
remote: Counting objects: 100% (49/49), done.
remote: Compressing objects: 100% (21/21), done.
remote: Total 37 (delta 30), reused 22 (delta 16), pack-reused 0
Unpacking objects: 100% (37/37), done.
From https://github.com/Clinical-Genomics/demultiplexing
   d5245ba..346c338  master     -> origin/master
 * [new branch]      fixing-demux-config-file -> origin/fixing-demux-config-file
 * [new tag]         5.11.0     -> 5.11.0
Branch fixing-demux-config-file set up to track remote branch fixing-demux-config-file from origin.
Switched to a new branch 'fixing-demux-config-file'
Already up-to-date.
/home/hiseq.clinical
No broken requirements found.
demux, version 5.10.5
cgstats, version 1.8.1
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
repository is clean
Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/hiseq.clinical
done.
Log deploy... done.
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
repository is clean
Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/hiseq.clinical
done.
Log deploy... done.

Testing demultiplexing with master


⌂21.76 θ84° 10d [hiseq.clinical@hasta:~] [S_base] 46s $ bash /home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.bash /home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY
[20230322101024] demuxtiles.bash VERSION 5.5.0
/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.bash: STAGE_CONDA_ENVS_PATH: unbound variable
beatrizsavinhas commented 1 year ago

Testing again

Installing branch on stage

13d [hiseq.clinical@hasta:~] [S_base] 5s $ bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-demux-stage.sh fixing-demux-config-file

Testing demultiplexing with master

13d [hiseq.clinical@hasta:/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY] [S_base] $ bash /home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.bash /home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY
[20230330094922] demuxtiles.bash VERSION 5.5.0
[20230330094922] /home/proj/stage/bin/miniconda3/bin/conda run --name S_demux /home/proj/stage/bin/miniconda3/envs/S_demux/bin/demux -c /home/proj/stage/servers/config/hasta.scilifelab.se/demux-stage.yaml sheet fetch -a wgs  HLCKNCCXY > /home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY/SampleSheet.csv
[20230330094937] /home/proj/stage/bin/miniconda3/bin/conda run --name S_demux /home/proj/stage/bin/miniconda3/envs/S_demux/bin/demux -c /home/proj/stage/servers/config/hasta.scilifelab.se/demux-stage.yaml sheet validate --application wgs /home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY/SampleSheet.csv
[20230330094940] Using sample sheet:
[Data]
FCID,Lane,SampleID,SampleRef,index,SampleName,Control,Recipe,Operator,Project
HLCKNCCXY,1,ACC4559A10_ATTACTCG,hg19,ATTACTCG,679810,N,R1,script,679810
HLCKNCCXY,2,ACC4559A3_TCCGGAGA,hg19,TCCGGAGA,679810,N,R1,script,679810
HLCKNCCXY,3,ACC4559A4_CGCTCATT,hg19,CGCTCATT,679810,N,R1,script,679810
HLCKNCCXY,4,ACC4559A11_GAGATTCC,hg19,GAGATTCC,679810,N,R1,script,679810
HLCKNCCXY,5,ACC4559A12_ATTCAGAA,hg19,ATTCAGAA,679810,N,R1,script,679810
HLCKNCCXY,6,ACC4556A2_TAATGCGC,hg19,TAATGCGC,272312,N,R1,script,272312
HLCKNCCXY,7,ACC4556A1_GAGATTCC,hg19,GAGATTCC,272312,N,R1,script,272312
HLCKNCCXY,8,ACC4554A1_ATTCAGAA,hg19,ATTCAGAA,126306,N,R1,script,126306
[20230330094940] Starting overall process
[20230330094940] starting lane 1 tile 11 12
[20230330094940] sbatch -A development -J 'Xdem-l1t11-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l1t11-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l1t11-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '1' 'stage' '11 12'
[20230330094940] Submitted batch job 4596561
[20230330094940] starting lane 1 tile 21 22
[20230330094940] sbatch -A development -J 'Xdem-l1t21-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l1t21-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l1t21-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '1' 'stage' '21 22'
[20230330094940] Submitted batch job 4596562
[20230330094940] starting lane 2 tile 11 12
[20230330094940] sbatch -A development -J 'Xdem-l2t11-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l2t11-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l2t11-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '2' 'stage' '11 12'
[20230330094940] Submitted batch job 4596563
[20230330094940] starting lane 2 tile 21 22
[20230330094940] sbatch -A development -J 'Xdem-l2t21-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l2t21-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l2t21-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '2' 'stage' '21 22'
[20230330094940] Submitted batch job 4596564
[20230330094940] starting lane 3 tile 11 12
[20230330094940] sbatch -A development -J 'Xdem-l3t11-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l3t11-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l3t11-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '3' 'stage' '11 12'
[20230330094940] Submitted batch job 4596565
[20230330094940] starting lane 3 tile 21 22
[20230330094940] sbatch -A development -J 'Xdem-l3t21-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l3t21-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l3t21-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '3' 'stage' '21 22'
[20230330094940] Submitted batch job 4596566
[20230330094940] starting lane 4 tile 11 12
[20230330094940] sbatch -A development -J 'Xdem-l4t11-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l4t11-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l4t11-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '4' 'stage' '11 12'
[20230330094940] Submitted batch job 4596567
[20230330094940] starting lane 4 tile 21 22
[20230330094940] sbatch -A development -J 'Xdem-l4t21-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l4t21-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l4t21-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '4' 'stage' '21 22'
[20230330094940] Submitted batch job 4596568
[20230330094940] starting lane 5 tile 11 12
[20230330094940] sbatch -A development -J 'Xdem-l5t11-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l5t11-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l5t11-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '5' 'stage' '11 12'
[20230330094941] Submitted batch job 4596569
[20230330094941] starting lane 5 tile 21 22
[20230330094941] sbatch -A development -J 'Xdem-l5t21-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l5t21-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l5t21-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '5' 'stage' '21 22'
[20230330094941] Submitted batch job 4596570
[20230330094941] starting lane 6 tile 11 12
[20230330094941] sbatch -A development -J 'Xdem-l6t11-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l6t11-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l6t11-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '6' 'stage' '11 12'
[20230330094941] Submitted batch job 4596571
[20230330094941] starting lane 6 tile 21 22
[20230330094941] sbatch -A development -J 'Xdem-l6t21-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l6t21-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l6t21-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '6' 'stage' '21 22'
[20230330094941] Submitted batch job 4596572
[20230330094941] starting lane 7 tile 11 12
[20230330094941] sbatch -A development -J 'Xdem-l7t11-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l7t11-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l7t11-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '7' 'stage' '11 12'
[20230330094941] Submitted batch job 4596573
[20230330094941] starting lane 7 tile 21 22
[20230330094941] sbatch -A development -J 'Xdem-l7t21-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l7t21-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l7t21-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '7' 'stage' '21 22'
[20230330094941] Submitted batch job 4596574
[20230330094941] starting lane 8 tile 11 12
[20230330094941] sbatch -A development -J 'Xdem-l8t11-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l8t11-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l8t11-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '8' 'stage' '11 12'
[20230330094941] Submitted batch job 4596575
[20230330094941] starting lane 8 tile 21 22
[20230330094941] sbatch -A development -J 'Xdem-l8t21-HLCKNCCXY' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l8t21-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/Xdem-l8t21-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xdemuxtiles.batch' '/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//' '8' 'stage' '21 22'
[20230330094941] Submitted batch job 4596576
[20230330094941] submit postface
[20230330094942] Running 4596563 4596564 4596565 4596566 4596567 4596568 4596569 4596570 4596571 4596572 4596573 4596574 4596575 4596576 4536435 4594870 4594874 4594876 4594879 4594884 4594894 4594895 4594896 4594868 4594869 4594872 4594873 4594875 4594878 4594880 4594882 4594883 4594885 4594886 4594887 4594888 4594890 4594891 4594892 4594897 4594898 4594899 4594900 4594901 4594902 4594903 4594904 4594905 4596561 4596562 4594865 4596537 4596538 4596535 4596536
[20230330094942] Demux 4596561 4596562 4596563 4596564 4596565 4596566 4596567 4596568 4596569 4596570 4596571 4596572 4596573 4596574 4596575 4596576
[20230330094942] Remaining 4596561 4596562 4596563 4596564 4596565 4596566 4596567 4596568 4596569 4596570 4596571 4596572 4596573 4596574 4596575 4596576
[20230330094942] sbatch -A development -J 'Xdem-postface' --dependency='afterok:4596561:4596562:4596563:4596564:4596565:4596566:4596567:4596568:4596569:4596570:4596571:4596572:4596573:4596574:4596575:4596576' -o '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/xdem-xpostface-HLCKNCCXY-%j.log' -e '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//LOG/xdem-xpostface-HLCKNCCXY-%j.err' '/home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xpostface.batch' '/home/proj/stage/demultiplexed-runs/180522_ST-E00198_0301_BHLCKNCCXY//'
Submitted batch job 4596577
[20230330094942] Everything started

SampleSheet.csv

13d [hiseq.clinical@hasta:/home/proj/stage/flowcells/hiseqx/180522_ST-E00198_0301_BHLCKNCCXY] [S_base] 8s $ cat SampleSheet.csv
[Data]
FCID,Lane,SampleID,SampleRef,index,SampleName,Control,Recipe,Operator,Project
HLCKNCCXY,1,ACC4559A10_ATTACTCG,hg19,ATTACTCG,679810,N,R1,script,679810
HLCKNCCXY,2,ACC4559A3_TCCGGAGA,hg19,TCCGGAGA,679810,N,R1,script,679810
HLCKNCCXY,3,ACC4559A4_CGCTCATT,hg19,CGCTCATT,679810,N,R1,script,679810
HLCKNCCXY,4,ACC4559A11_GAGATTCC,hg19,GAGATTCC,679810,N,R1,script,679810
HLCKNCCXY,5,ACC4559A12_ATTCAGAA,hg19,ATTCAGAA,679810,N,R1,script,679810
HLCKNCCXY,6,ACC4556A2_TAATGCGC,hg19,TAATGCGC,272312,N,R1,script,272312
HLCKNCCXY,7,ACC4556A1_GAGATTCC,hg19,GAGATTCC,272312,N,R1,script,272312
HLCKNCCXY,8,ACC4554A1_ATTCAGAA,hg19,ATTCAGAA,126306,N,R1,script,126306