excap_31

Excap 31

Sample	mapping group	variant group	NSC delivered	mapping started	mapping finished	variant started	variant finished	SNP-ID	delivered
14000670001-EEogPU	NA	NA	13/10/14 18:42	14/10/14 09:47:11	15/10/14 09:04:38	15/10/14 09:20:14	16/10/14 05:14:41	OK	21/10/14 08:00:00
14000670200-EEogPU	NA	NA	13/10/14 18:42	14/10/14 09:49:37	15/10/14 06:33:53	15/10/14 08:15:00	16/10/14 03:02:28	OK	21/10/14 08:00:00
14000700101-EEogPU	NA	NA	13/10/14 18:42	14/10/14 09:50:45	15/10/14 06:29:08	15/10/14 08:17:00	16/10/14 02:52:18	3 failed rs3108237 rs1700490 rs9958735	21/10/14 08:00:00
14000759601-EEogPU	NA	NA	13/10/14 18:42	15/10/14 08:35:22	16/10/14 10:21:03	16/10/14 10:23:59	17/10/14 08:14:15	OK	21/10/14 08:00:00
13000080601-EEogPU	1	NA	13/10/14 18:42	14/10/14 09:44:43	15/10/14 11:11:40	15/10/14 11:17:48	16/10/14 06:22:00	1 failed rs33910368	21/10/14 08:00:00
14000672201-EEogPU	1	NA	13/10/14 18:42	15/10/14 23:40:37	16/10/14 22:28:54	17/10/14 10:37:37	18/10/14 09:37:30	OK	21/10/14 08:00:00
14000680301-EEogPU	1	NA	13/10/14 18:42	16/10/14 22:28:54	17/10/14 23:36:30	18/10/14 13:10:08	19/10/14 07:42:06	OK	21/10/14 08:00:00
14000694201-EEogPU	1	NA	13/10/14 18:42	17/10/14 23:36:31	19/10/14 00:53:47	19/10/14 15:12:21	27/10/14 11:35:58	2 failed rs257376 rs3851
14000701801-EEogPU	2	NA	13/10/14 18:42	15/10/14 03:24:47	16/10/14 03:03:40	16/10/14 08:25:00	17/10/14 04:39:25	3 failed rs1137288 rs1700490 rs3851	21/10/14 08:00:00
14000718001-EEogPU	2	NA	13/10/14 18:42	16/10/14 03:03:41	17/10/14 04:37:56	17/10/14 10:40:25	18/10/14 09:47:49	OK	21/10/14 08:00:00
14000723501-EEogPU	2	NA	13/10/14 18:42	17/10/14 04:37:56	18/10/14 05:51:47	18/10/14 13:12:45	19/10/14 07:52:55	OK	21/10/14 08:00:00
14000730301-EEogPU	2	NA	13/10/14 18:42	18/10/14 05:51:48	19/10/14 06:21:44	19/10/14 15:17:34	20/10/14 08:06:14	OK	21/10/14 08:00:00
14000759401-EEogPU	3	NA	13/10/14 18:42	15/10/14 03:25:44	16/10/14 03:26:26	16/10/14 08:28:14	17/10/14 05:30:14	OK	21/10/14 08:00:00
14000769401-EEogPU	3	NA	13/10/14 18:42	16/10/14 03:26:26	17/10/14 05:21:01	17/10/14 10:43:43	18/10/14 10:10:16	OK	21/10/14 08:00:00
14000771301-EEogPU	3	NA	13/10/14 18:42	17/10/14 05:21:01	18/10/14 07:33:04	18/10/14 13:15:58	19/10/14 07:10:27	1 failed rs33910368	21/10/14 08:00:00
14000775601-EEogPU	3	NA	13/10/14 18:42	18/10/14 07:33:04	19/10/14 08:34:56	19/10/14 15:18:40	20/10/14 08:12:35	OK	21/10/14 08:00:00
14000608001-PCD	NA	NA	13/10/14 18:42	15/10/14 12:48:07	17/10/14 13:05:30	17/10/14 13:14:33	19/10/14 01:12:48	OK	21/10/14 08:00:00
14000659901-PCD	NA	NA	13/10/14 18:42	17/10/14 13:05:30	19/10/14 15:01:26	19/10/14 15:20:00	20/10/14 22:52:26	OK	21/10/14 08:00:00

15/10/2014

Should I call the variant as the files appears, meaning if I am in front of the computer and the mapping is finished should I start the variant calling only on this file???

16/10/2014

doing variant calling as files are coming….

19/20/2014

mapping1.sh

real 5789m53.536s user 31779m9.082s sys 77m15.175s

mapping2.sh

real 5936m57.663s user 32463m37.724s sys 85m37.856s

mapping3.sh

real 6069m11.667s user 34106m21.715s sys 91m28.643s

20/10/2014

Sample_Diag-excap31-14000694201-EEogPU-v01-KIT-Av5

failed twice

Current work directory:
/data/diag/diagInternal/samples/141003_7001448.A.Project_Diag-excap31-2014-09-26/Sample_Diag-excap31-14000694201-EEogPU-v01-KIT-Av5/030_postAlignQC
Doing collectAlignmentSummaryMetrics ... start at -----	Sun Oct 19 15:15:34 CEST 2014
OpenJDK 64-Bit Server VM warning: You have loaded library /data/diag/diagInternal/diagnosticBundle/tools/picard-tools-1.107/picard-tools-1.107/libIntelDeflater.so which might have disabled stack guard. The VM will try to fix the stack guard now.
It's highly recommended that you fix the library with 'execstack -c ', or link it with '-z noexecstack'.
Died at /data/diag/diagInternal/diagnosticBundle/script/amg_test/variantcalling/pipeline/pipeline_current/steps/parseMetrics.pl line 15.
####################
CollectAlignmentSummaryMetrics is failed
####################
grep: 030_calculateHsMetrics/calculateHsMetrics.easy.txt: No such file or directory
Use of uninitialized value $offBait in pattern match (m//) at /data/diag/diagInternal/diagnosticBundle/script/amg_test/variantcalling/pipeline/pipeline_current/variantCallingPipeline.pl line 366.
grep: 030_calculateHsMetrics/calculateHsMetrics.easy.txt: No such file or directory
Use of uninitialized value $pfuqReadsAligned in division (/) at /data/diag/diagInternal/diagnosticBundle/script/amg_test/variantcalling/pipeline/pipeline_current/variantCallingPipeline.pl line 374.
Illegal division by zero at /data/diag/diagInternal/diagnosticBundle/script/amg_test/variantcalling/pipeline/pipeline_current/variantCallingPipeline.pl line 374.

27/10/2014

delete /data/diag/diagInternal/samples/141003_7001448.A.Project_Diag-excap31-2014-09-26/Sample_Diag-excap31-14000694201-EEogPU-v01-KIT-Av5/030_postAlignQC

and rerun