Skip to content

Project_Diag excap22 2014 03 24

Jump to bottom Edit New page
yvan edited this page Apr 16, 2014 · 5 revisions

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 | Sample_Diag-excap22-14000152900-HSPogHA-KIT-Av5 | 07.04.2014 | 07.04.2014 | 08.04.2014 | 10.04.2014 | 10.04.2014 @ 09:10 | 10.04.2014 @ 21:45 | pass / 2 Taq undeter. | 14.04.2014 | | 2 | Sample_Diag-excap22-14000153000-HSPogHA-KIT-Av5 | 07.04.2014 | 07.04.2014 | 08.04.2014 | 10.04.2014 | 10.04.2014 @ 21:45 | 11.04.2014 @ 11:15 | pass / 3 Taq undeter. | 14.04.2014 | | 3 | Sample_Diag-excap22-14000153500-HSPogHA-KIT-Av5 | 07.04.2014 | 07.04.2014 | 08.04.2014 | 09.04.2014 | 11.04.2014 @ 11:15 | 11.04.2014 @ ? | pass / 2 underter. | 14.04.2014 |

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…..
    • Sorte is doing also some mapping it is why it takes so long
    • Don't forget to rerun the generateCMDmappingCondor.pl script
pcus572:Project_Diag-excap22-2014-03-24 yvans$ !11
perl /Volumes/data.odin/diagnosticBundle/script/amg/variantcalling/pipeline/pipeline_current/generateCMDmappingCondor.pl


#######################


The script you are running now is only for Research purpose and for no other purpose.


#######################



1, Please copy all the fastq files from run folder to /condor_sh/projects; the folder structure should be the same as the original run folder, e.g. Project_excap/Sample_excap1/*.fastq.gz

2, Log into Tor as root,

change the permission by:
chmod -R 777 Project_excap

change owner, group as SBSUser by:
chown -R SBSUser:SBSUser Project_excap

3, log out from root

If you haven't done the above, you can stop this script now and run it again when it is ready, otherwise press return


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

Project_Diag-excap22-2014-03-24

Making the folder structure in the condor required data structure and generate mapping commands (saved in commandMapping.bash under each sample/data) ......

A sample configuration file (sampleMac.conf) is also generated in the same folder to start further analysis after alignment
A group configuration file (groupMac.conf) is generated under the Project folder, which can be used for running analysis on a batch of samples


Please input the full path to the diagnosticBundle, the default is "/Volumes/data.odin/diagnosticBundle" if you just press return



Please input the full path to the dataDistro, the default is "/Volumes/data.odin/diagnosticBundle/refData/dataDistro_r01_d01_diag" if you just press return



Please input the full path to the script folder (git local copy), the default is "/Volumes/data.odin/diagnosticBundle/script/amg/variantcalling/pipeline/pipeline_current" if you just press return


Please input the full path to the software folder, the default is "/Volumes/data.odin/diagnosticBundle/tools" if you just press return


Working on sample Sample_Diag-excap22-14000152900-HSPogHA-KIT-Av5 --- data folder is already existed, will not move the fastq files *****

Done!
Working on sample Sample_Diag-excap22-14000153000-HSPogHA-KIT-Av5 --- data folder is already existed, will not move the fastq files *****

Done!
Working on sample Sample_Diag-excap22-14000153500-HSPogHA-KIT-Av5 --- data folder is already existed, will not move the fastq files *****

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

Good Luck!

  • Start variantcalling pipeline

    • Thu 10 Apr 2014 09:10:03
    • pcus572:Project_Diag-excap22-2014-03-24 yvans$ perl /Volumes/data.odin/diagnosticBundle/script/amg/variantcalling/pipeline/pipeline_current/runGroupPipeline.pl /condor_sh/projects/Project_Diag-excap22-2014-03-24/group.conf
    • Morning 11 Apr 2014 condor was taking all memory had to kill it
    • samtofastq also took a fair bit of cpu …
    • Errors form coverage scripts…. Accroding to Ying some coverage files wehre missing. NEED TO RERUN the pipeline when averything is finished
    • variant pipeline code was faulty, Ying rerun it after she merge the pull request from Tony.
    • Results delivered the 14.04.2014
Add a custom footer
Add a custom sidebar

Clone this wiki locally