Project_Diag excap22 2014 03 24

sequencing run 140305_D00132_0066_AC3U4PACXX - Project_Diag-excap22-2014-03-24

| 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 | | 1 | yvan | 07.04.14 | 07.04.14 | ? | ? | ? | ? | ? | ? | | 2 | yvan | 07.04.14 | 07.04.14 | ? | ? | ? | ? | ? | ? | | 3 | yvan | 07.04.14 | 07.04.14 | ? | ? | ? | ? | ? | ? |

Procedure

• Copy file to condor

  • rsync -avz Sample_Diag-excap22-1400015* /condor_sh/projects/Project_Diag-excap22-2014-03-24/

• Change ownership

  • log into tor

  root@tor:/condor_sh/projects #chmod -R 777 Project_Diag-excap22-2014-03-24/

  root@tor:/condor_sh/projects #chown -R SBSUser:SBSUser Project_Diag-excap22-2014-03-24/

  • 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-excap22-2014-03-24

  Working on sample Sample_Diag-excap22-14000152900-HSPogHA-KIT-Av5 --- Can not find /HSPogHA_OUS_medGen_v01_b37 for genePanel

  Done!

  Working on sample Sample_Diag-excap22-14000153000-HSPogHA-KIT-Av5 --- Can not find /HSPogHA_OUS_medGen_v01_b37 for genePanel

  Done!

  Working on sample Sample_Diag-excap22-14000153500-HSPogHA-KIT-Av5 --- Can not find /HSPogHA_OUS_medGen_v01_b37 for genePanel

  Done!

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

###!!!!Sending email about the genepanel HSPogHA!!!!

* [[condor job 08-04-2014]]

• Check if everything went alright

  • Something seems to went bad! Next time save job number to track them down….

• Start variantcalling pipeline

  • ?