sequencing run 140305_D00132_0066_AC3U4PACXX Project_Diag excap20 2014 02 24 - yvancouver/Workflow GitHub Wiki

sequencing run 140305_D00132_0066_AC3U4PACXX - Project_Diag-excap20-2014-02-24

| file | reps. | mail form Arvind | condor moved | condor started | condor finished | Variant calling Started | Variant calling Finished | Snp test | Delivery | | :-----------------------------------------------: | :---------------------------: | :-----: | :--------: | :------: | :------: | :------: | :------: | :------: | :------: |:------: | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | | Sample_Diag-excap20-13001130200-EE-KIT-Av5 | yvan | 19.3.14 | 21.3.14 | 21.3.14 | 24.3.14 | 24.3.2014 @ 10:45 | 24.3.2014 @22:00 | pass | GOOD 26.3.2014 | | Sample_Diag-excap20-13001139400-EE-KIT-Av5 | yvan | 19.3.14 | 21.3.14 | 21.3.14 | 24.3.14 | 25.3.2014 @ 22:00 | 25.3.2014 @ 8:30 | pass | GOOD 26.3.2014 | | Sample_Diag-excap20-13001157000-PCD-KIT-Av5 | yvan | 19.3.14 | 21.3.14 | 21.3.14 | 24.3.14 | 25.3.2014 @ 8:40 | 25.03.2014 @ 18:10 | pass | GOOD 01.3.2014 | | Sample_Diag-excap20-13001157200-EE-KIT-Av5 | yvan | 19.3.14 | 21.3.14 | 21.3.14 | 24.3.14 | 24.3.2014 @ 11:00| 24.3.2014 @ 22:30 | pass | GOOD 26.3.2014 | | Sample_Diag-excap20-13001172200-Bindevev-KIT-Av5 | yvan | 19.3.14 | 21.3.14 | 21.3.14 | 24.3.14 | 24.3.2014 @ 23:40 | 25.3.2014 @ 09:15 | pass | GOOD 26.3.2014 | | Sample_Diag-excap20-13001173300-EE-KIT-Av5 | yvan | 19.3.14 | 21.3.14 | 21.3.14 | 24.3.14 | 24.3.2014 @ 22:30 | ERRORS | Not Done | RERUN | | Sample_Diag-excap20-13001173300-EE-KIT-Av5 RERUN | yvan | 19.3.14 | 21.3.14 | 21.3.14 | 24.3.14 | 25.3.2014 @ 11:00 | 25.3.2014 @ 21:15 | pass | GOOD 26.3.2014 |

Procedure

• Copy file to condor

  • pcus572:Project_Diag-excap20-2014-02-24 yvans$ rsync -rRuaP /Volumes/runScratch/140305_D00132_0066_AC3U4PACXX/Unaligned_lane245678/140305_D00132.A.Project_Diag-excap20-2014-02-24/ /condor_sh/projects/Project_Diag-excap20-2014-02-24/

    Don't put full path in rsync it will just recreate the file system

  • mv the Sample back to Project_Diag-excap20-2014-02-24

• Change ownership

  • log into tor

  root@tor:/condor_sh/projects #chmod -R 777 Project_Diag-excap20-2014-02-24/

  root@tor:/condor_sh/projects #chown -R SBSUser:SBSUser Project_Diag-excap20-2014-02-24/

  • log out

• Run the generateCMD script

  • perl /Volumes/data.odin/diagnosticBundle/script/amg/variantcalling/pipeline/pipeline_current/generateCMDmappingCondor.pl

  After all the files have been transferred, Input the project name, in this case - Project_excap

  Project_Diag-excap20-2014-02-24

  Working on sample Sample_Diag-excap20-13001130200-EE-KIT-Av5 --- Done!

  Working on sample Sample_Diag-excap20-13001139400-EE-KIT-Av5 --- Done!

  Working on sample Sample_Diag-excap20-13001157000-PCD-KIT-Av5 --- Done!

  Working on sample Sample_Diag-excap20-13001157200-EE-KIT-Av5 --- Done!

  Working on sample Sample_Diag-excap20-13001172200-Bindevev-KIT-Av5 --- Done!

  Working on sample Sample_Diag-excap20-13001173300-EE-KIT-Av5 --- Done!

  Now you can go into tor and run each commandMapping.bash file

  • condor job 20-2014-02-24

• Check if everything went alright

  • 24/03/2014 seems ok at least size wise

• Start variantcalling pipeline

  • Split the group.conf in two: group-1.conf and group-2.conf on /projects/
  • Make a folder Project_Diag-excap20-2014-02-24
  • perl variantcalling/pipeline/pipeline_current/.pl group-1.conf