excap36

excap36

####24 Feb 2015

1. Make 4 groups of 4 samples

group1.conf

Sample_Diag-excap36-13000895501-Bindevev-v01-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-13000895501-Bindevev-v01-KIT-Av5/data/sample.conf
Sample_Diag-excap36-13001048001-EEogPU-v02-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-13001048001-EEogPU-v02-KIT-Av5/data/sample.conf
Sample_Diag-excap36-13001112702-Bindevev-v01-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-13001112702-Bindevev-v01-KIT-Av5/data/sample.conf
Sample_Diag-excap36-14000604801-Bindevev-v01-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-14000604801-Bindevev-v01-KIT-Av5/data/sample.conf

group1.conf (END)

group2.conf

Sample_Diag-excap36-14000707901-EEogPU-v02-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-14000707901-EEogPU-v02-KIT-Av5/data/sample.conf
Sample_Diag-excap36-14000958104-Mitokon-v01-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-14000958104-Mitokon-v01-KIT-Av5/data/sample.conf
Sample_Diag-excap36-14001120900-EEogPU-v02-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-14001120900-EEogPU-v02-KIT-Av5/data/sample.conf
Sample_Diag-excap36-14001139400-EEogPU-V02-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-14001139400-EEogPU-V02-KIT-Av5/data/sample.conf

group2.conf (END)

group3.conf

Sample_Diag-excap36-14001139501-EEogPU-v02-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-14001139501-EEogPU-v02-KIT-Av5/data/sample.conf
Sample_Diag-excap36-14001189601-Bindevev-v01-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-14001189601-Bindevev-v01-KIT-Av5/data/sample.conf
Sample_Diag-excap36-14001196101-Bindevev-v01-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-14001196101-Bindevev-v01-KIT-Av5/data/sample.conf
Sample_Diag-excap36-14001199901-EEogPU-v02-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-14001199901-EEogPU-v02-KIT-Av5/data/sample.conf

group3.conf (END)

group4.conf

Sample_Diag-excap36-14001203001-EEogPU-v02-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-14001203001-EEogPU-v02-KIT-Av5/data/sample.conf
Sample_Diag-excap36-14001219901-Bindevev-v01-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-14001219901-Bindevev-v01-KIT-Av5/data/sample.conf
Sample_Diag-excap36-14001229301-EEogPU-v02-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-14001229301-EEogPU-v02-KIT-Av5/data/sample.conf
Sample_Diag-excap36-14001245201-PCD-v01-KIT-Av5 /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-14001245201-PCD-v01-KIT-Av5/data/sample.conf

group4.conf (END)

2. Activate python27

scl enable python27 bash

source /data/common/system/python27/bin/activate

3. run pipeline

errors see group1.log file

FIX this is due to the copy paste operation which change tab with spaces... correct the .conf files and rerun 4. run one sample to test the setup.

bash-4.1$ cd Sample_Diag-excap36-13000895501-Bindevev-v01-KIT-Av5/
bash-4.1$ perl /data/diag/diagInternal/diagnosticBundle/script/amg/variantcalling/pipeline/variantCallingPipeline.pl /data/diag/diagInternal/samples/150209_D00132.A.Project_Diag-excap36-2015-01-27/Sample_Diag-excap36-13000895501-Bindevev-v01-KIT-Av5/data/sample.conf &> Sample_Diag-excap36-13000895501-Bindevev-v01-KIT-Av5.log

####25 Feb 2015

Sample	group	variant calling	checkerrors
Sample_Diag-excap36-13000895501-Bindevev-v01-KIT-Av5	1	Finish 2 mismatch rs3736782 (HTS A/C 175 87A/88C Taq A:A/A), rs2241802 (HTS G/G 252 250G/2A Taq R:A/G)	Postprocess done
Sample_Diag-excap36-13001048001-EEogPU-v02-KIT-Av5	1	Finish OK	Postprocess done
Sample_Diag-excap36-13001112702-Bindevev-v01-KIT-Av5	1	Finish 2 mismatch rs3736782 rs2241802
Sample_Diag-excap36-14000604801-Bindevev-v01-KIT-Av5	1	Finish OK
Sample_Diag-excap36-14000707901-EEogPU-v02-KIT-Av5	2	Finish OK	Postprocess done
Sample_Diag-excap36-14000958104-Mitokon-v01-KIT-Av5	2	Finish 2 mismatch rs3736782 rs2241802
Sample_Diag-excap36-14001120900-EEogPU-v02-KIT-Av5	2	Finish 2 mismatch rs3736782 rs2241802
Sample_Diag-excap36-14001139400-EEogPU-V02-KIT-Av5	2	Finish OK
Sample_Diag-excap36-14001139501-EEogPU-v02-KIT-Av5	3	Finish 2 mismatch rs3736782 (HTS C:C/C 213 213C Taq M:A/C), rs2241802 (HTS R:A/G 207 112A/94G Taq A:A/A)	Postprocess done
Sample_Diag-excap36-14001189601-Bindevev-v01-KIT-Av5	3	Finish 2 mismatch rs3736782 rs2241802
Sample_Diag-excap36-14001196101-Bindevev-v01-KIT-Av5	3	Finish 1 mismatch rs2241802
Sample_Diag-excap36-14001199901-EEogPU-v02-KIT-Av5	3	Finish 1 mismatch rs3736782
Sample_Diag-excap36-14001203001-EEogPU-v02-KIT-Av5	4	Finish 1 mismatch rs2241802 (HTS R:A/G 227 116A 111G Taq A:A/A)	Postprocess done
Sample_Diag-excap36-14001219901-Bindevev-v01-KIT-Av5	4	Finish OK
Sample_Diag-excap36-14001229301-EEogPU-v02-KIT-Av5	4	Finish 1 mismatch rs2241802
Sample_Diag-excap36-14001245201-PCD-v01-KIT-Av5	4	Finish 1 mismatch rs2241802

####26 Feb 2015

Everything crashed , permission errors and faulty pipeline, see reportPostAlignProcess.txt where the post calibration failed.

Ying is debugging it with the sample Sample_Diag-excap36-13001048001-EEogPU-v02-KIT-Av5

Restart the four groups.