excap_30

Excap 30

Sample	mapping group	variant group	NSC delivered	mapping started	mapping finished	variant started	variant finished	SNP-ID	delivered
NA12878	no	no	25/09/14 12:00:00	26/09/14 09:17:38	27/09/14 17:51:57	29/09/14 08:26:12	30/09/14 03:39:56	OK	06/10/14 12:00:00
13001117101	13	no	25/09/14 12:00:00	30/09/14 02:01:38	01/10/14 02:47:05	01/10/14 14:28:00	02/10/14 06:14:22	OK	06/10/14 12:00:00
14000474800	14a	no	25/09/14 12:00:00	01/10/14 05:08:20	02/10/14 06:46:43	02/10/14 14:12:26	03/10/14 07:59:32	OK	06/10/14 12:00:00
14000660001	14c	1	25/09/14 12:00:00	26/09/14 09:58:38	27/09/14 08:37:07	30/09/14 08:29:50	01/10/14 04:55:13	OK	06/10/14 12:00:00
13001005002dup	13	1	25/09/14 12:00:00	27/09/14 18:12:42	28/09/14 12:05:57	01/10/14 04:58:06	01/10/14 18:34:07	Failed no ID found	07/10/14 08:00:00
14000071001	14a	1	25/09/14 12:00:00	27/09/14 17:03:30	28/09/14 15:06:11	29/09/14 13:55:45	30/09/14 08:26:29	OK	06/10/14 12:00:00
13000291602dup	13	1	25/09/14 12:00:00	26/09/14 09:27:13	27/09/14 14:18:25	01/10/14 18:37:35	02/10/14 12:48:01	Failed no ID found	07/10/14 08:00:00
14000505801	14b	1	25/09/14 12:00:00	26/09/14 09:57:41	27/09/14 09:46:29	02/10/14 12:50:15	03/10/14 08:19:46	OK	06/10/14 12:00:00
14000015802	14a	1	25/09/14 12:00:00	26/09/14 09:47:19	27/09/14 13:01:02	03/10/14 08:22:29	04/10/14 04:50:07	OK	06/10/14 12:00:00
14000662301	14c	2	25/09/14 12:00:00	27/09/14 12:13:48	28/09/14 07:35:53	01/10/14 17:31:40	02/10/14 10:23:24	OK	06/10/14 12:00:00
14000516800	14b	2	25/09/14 12:00:00	27/09/14 13:22:23	28/09/14 15:49:04	30/09/14 11:32:00	01/10/14 08:06:15	OK	06/10/14 12:00:00
13001005002	13	2	25/09/14 12:00:00	28/09/14 14:33:12	29/09/14 22:52:35	02/10/14 10:25:38	03/10/14 03:08:11	OK	06/10/14 12:00:00
14000694001	14c	2	25/09/14 12:00:00	28/09/14 10:49:08	29/09/14 04:48:01	03/10/14 03:10:17	03/10/14 19:58:15	FAILED MISMATCH	07/10/14 08:00:00
14000520100dup	14b	2	25/09/14 12:00:00	28/09/14 19:12:46	29/09/14 13:54:39	03/10/14 19:59:47	04/10/14 09:27:31	Failed no ID found	07/10/14 08:00:00
14000337103	14a	2	25/09/14 12:00:00	28/09/14 18:25:58	29/09/14 18:27:15	04/10/14 09:29:27	05/10/14 00:30:15	OK	06/10/14 12:00:00
14000580601	14b	3	25/09/14 12:00:00	30/09/14 14:59:03	01/10/14 22:30:07	02/10/14 08:29:40	03/10/14 04:04:11	OK	06/10/14 12:00:00
14000455300	14a	3	25/09/14 12:00:00	29/09/14 22:00:34	01/10/14 01:41:07	03/10/14 04:06:18	03/10/14 21:01:46	OK	06/10/14 12:00:00
14000770901	14c	3	25/09/14 12:00:00	29/09/14 07:48:12	30/09/14 09:10:08	05/10/14 06:43:46	06/10/14 00:21:47	OK	06/10/14 12:00:00
14000776001	14c	3	25/09/14 12:00:00	30/09/14 13:26:42	01/10/14 14:20:33	03/10/14 21:04:14	04/10/14 15:07:01	OK	06/10/14 12:00:00
14000537201	14b	3	25/09/14 12:00:00	29/09/14 16:43:32	30/09/14 11:27:34	04/10/14 15:09:04	05/10/14 06:41:20	OK	06/10/14 12:00:00
14000479600	14a	4	25/09/14 12:00:00	02/10/14 10:03:19	03/10/14 11:07:43	06/10/14 10:07:16	06/10/14 23:32:24	OK	07/10/14 08:00:00
14000798301	14c	4	25/09/14 12:00:00	03/10/14 11:53:22	04/10/14 07:08:07	04/10/14 18:44:54	05/10/14 10:24:15	OK	06/10/14 12:00:00
14000651701	14b	no	25/09/14 12:00:00	02/10/14 02:09:35	02/10/14 19:48:46	03/10/14 10:47:47	04/10/14 03:56:15	OK	06/10/14 12:00:00
14000787501	14c	no	25/09/14 12:00:00	02/10/14 08:43:36	03/10/14 08:10:27	03/10/14 11:57:08	04/10/14 07:54:21	OK	06/10/14 12:00:00

###Mapping

mapping group
13	14a	14b	14c
13000291602dup	14000015802	14000505801	14000660001
13001005002dup	14000071001	14000516800	14000662301
13001005002	14000337103	14000520100dup	14000694001
13001117101	14000455300	14000537201	14000770901
	14000474800	14000580601	14000776001
	14000479600	14000651701	14000787501
			14000798301

###Variant calling

variant.group1.conf	variant.group2.conf	variant.group3.conf	variant.group3.conf
13000291602dup	14000516800	14000455300	14000479600
14000015802	14000662301	14000537201	14000798301
14000505801	13001005002	14000770901
14000660001	14000337103	14000580601
13001005002dup	14000520100dup	14000776001
14000071001	14000694001

###29/09/2014

error in the pipeline:

Start to refine HGMD annotation ----- Wed Oct  1 10:05:20 CEST 2014

 Start to add HGVS intronic position ----- Wed Oct  1 10:05:20 CEST 2014
Traceback (most recent call last):
  File "/data/diag/diagInternal/diagnosticBundle/script/amg_test/annotation/pipeline/add_hgvs.py", line 24, in 
    from annotation.util import coordinates
ImportError: No module named annotation.util

Start to add in-house db frequency and find the right transcript ----- Wed Oct  1 10:05:20 CEST 2014
Died at /data/diag/diagInternal/diagnosticBundle/script/amg_test/variantcalling/pipeline/pipeline_current/steps/refineAnnotation.pl line 116.
########### Comparing snp finger printing results betwen HTS and Taqman ......

python: can't open file '/data/diag/diagInternal/diagnosticBundle/script/amg/fingerprinting/testData/MergeResults.py': [Errno 2] No such file or directory
cp: cannot stat `070_QC/snp.raw.snpFingerPrintingTest*report*': No such file or directory
The script is finished

Send an email to Ying waiting for the corrections

###01/10/2014

Change the sample.conf in

yvans@loki:/data/diag/diagInternal/samples/140916_7001448.A.Project_Diag-excap30-2014-09-09
> cp Sample_Diag-excap30-14000455300-VaBindevev-v01-KIT-Av5/data/sample.conf Sample_Diag-excap30-14000455300-VaBindevev-v01-KIT-Av5/data/sample_ori.conf

Rerun NA12878

01/10/14 12:57:54 perl /data/diag/diagInternal/diagnosticBundle/script/amg_test/variantcalling/pipeline/pipeline_current/variantCallingPipeline.check.pl /data/diag/diagInternal/samples/140916_7001448.A.Project_Diag-excap30-2014-09-09/Sample_Diag-excap30-NA12878-EEogPU-v01-KIT-Av5/data/sample.conf &> Sample_Diag-excap30-NA12878-EEogPU-v01-KIT-Av5_4.log

###02/10/2014

mapping group 14c

> time ./mappingExcap30_Samples14c.sh &> mappingExcap30_Samples14c.log

real	7676m28.051s
user	46531m11.888s
sys	111m3.877s

###03/10/14

mapping 14b

yvans@loki:/data/diag/diagInternal/samples/140916_7001448.A.Project_Diag-excap30-2014-09-09

> time ./mappingExcap30_Samples14b.sh &> mappingExcap30_Samples14b.log
real	9431m33.118s  
user	55543m40.419s
sys	155m22.281s  

####Errors in pipeline

Sample Sample_Diag-excap30-14000505801-Bindevev

Start to add in-house db frequency and find the right transcript ----- Fri Oct  3 08:19:43 CEST 2014
Can't open perl script "/data/diag/diagInternal/diagnosticBundle/script/amg_test/variantcalling/pipeline/pipeline_current/steps/refineAnnotation.pl": Permission denied
cp: cannot stat `allAnnotationInCand.hg19_multianno.freq.txt': No such file or directory

Sample Sample_Diag-excap30-14000580601-EEogPU

Start to add in-house db frequency and find the right transcript ----- Fri Oct  3 04:04:07 CEST 2014
Can't open perl script "/data/diag/diagInternal/diagnosticBundle/script/amg_test/variantcalling/pipeline/pipeline_current/steps/refineAnnotation.pl": Permission denied
cp: cannot stat `allAnnotationInCand.hg19_multianno.freq.txt': No such file or directory

Sample Sample_Diag-excap30-14000474800-Bindevev-

Start to add in-house db frequency and find the right transcript ----- Fri Oct  3 07:59:28 CEST 2014
Can't open perl script "/data/diag/diagInternal/diagnosticBundle/script/amg_test/variantcalling/pipeline/pipeline_current/steps/refineAnnotation.pl": Permission denied
cp: cannot stat `allAnnotationInCand.hg19_multianno.freq.txt': No such file or directory

Test post process script

1. mv NA12878 to tmp folder
2. Check and fix ownership and permissions
3. run the post process.pl

03/10/14 09:13:57 mkdir ../TestPostProcess
03/10/14 09:14:16 cp Sample_Diag-excap30-NA12878-EEogPU-v01-KIT-Av5 ../TestPostProcess/
03/10/14 09:14:22 cp -r Sample_Diag-excap30-NA12878-EEogPU-v01-KIT-Av5 ../TestPostProcess/
03/10/14 09:36:02 cd ../TestPostProcess/
03/10/14 09:36:19 chgrp -R ous-diag ./
03/10/14 09:36:28 chmod 770 -R ./
03/10/14 09:36:41 find ./ -group yvans
03/10/14 09:37:20 perl /data/diag/diagInternal/diagnosticBundle/script/amg_test/variantcalling/pipeline/pipeline_current/postProcess.pl

Everything went well

####06/10/14
Rerun group3 because of error in sample Sample_Diag-excap30-14000580601-EEogPU
Rerun group2 because of errors
Rerun group1 because of errors in Sample_Diag-excap30-14000505801-Bindevev