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excap_33
yvan edited this page Mar 18, 2015
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| Sample | mapping group | NSC delivered | mapping started | mapping finished | variant started | variant finished | SNP-ID | delivered |
|---|---|---|---|---|---|---|---|---|
| 13000312105 | 1 | 06/11/14 09:23:00 | 07/11/14 09:01:15 | 08/11/14 15:17:27 | 10/11/14 12:52:52 | 11/11/14 10:44:24 | OK | 11/11/14 13:30:00 |
| 14000874700 | 2 | 06/11/14 09:23:00 | 07/11/14 09:06:15 | 08/11/14 15:49:56 | 10/11/14 15:40:34 | 11/11/14 11:32:42 | OK | 11/11/14 13:30:00 |
| 14000912100 | 3 | 06/11/14 09:23:00 | 07/11/14 09:11:47 | 08/11/14 16:12:51 | 10/11/14 15:44:20 | 12/11/14 06:43:38 | OK | 12/11/14 12:00:00 |
| 14000881700 | 2 | 06/11/14 09:23:00 | 08/11/14 15:49:57 | 09/11/14 19:37:04 | 10/11/14 15:47:50 | 11/11/14 12:06:37 | OK | 11/11/14 13:30:00 |
| 14000912600 | 3 | 06/11/14 09:23:00 | 08/11/14 16:12:51 | 09/11/14 23:17:13 | 10/11/14 15:54:50 | 11/11/14 13:14:06 | OK | 11/11/14 13:40:00 |
| 13000343602 | 1 | 06/11/14 09:23:00 | 08/11/14 15:17:28 | 10/11/14 03:37:30 | 11/11/14 13:02:30 | 12/11/14 15:25:52 | OK | 12/11/14 15:30:00 |
| 14000882400 | 2 | 06/11/14 09:23:00 | 09/11/14 19:37:05 | 10/11/14 23:48:38 | 11/11/14 13:05:25 | 12/11/14 08:27:44 | OK | 12/11/14 12:00:00 |
| 14000913100 | 3 | 06/11/14 09:23:00 | 09/11/14 23:17:14 | 11/11/14 07:08:55 | 11/11/14 13:07:09 | 12/11/14 08:06:02 | OK | 12/11/14 12:00:00 |
| 13001128402 | 1 | 06/11/14 09:23:00 | 10/11/14 03:37:30 | 11/11/14 21:15:12 | 12/11/14 08:34:37 | 13/11/14 09:11:23 | OK | 13/11/14 11:30:00 |
| 14000886003 | 2 | 06/11/14 09:23:00 | 10/11/14 23:48:39 | 12/11/14 09:34:29 | 12/11/14 09:35:45 | 13/11/14 05:01:23 | OK | 13/11/14 11:30:00 |
| 14000918100 | 3 | 06/11/14 09:23:00 | 11/11/14 07:08:55 | 12/11/14 13:58:49 | 12/11/14 14:02:22 | 13/11/14 08:10:40 | OK | 13/11/14 11:30:00 |
| 14000176900 | 1 | 06/11/14 09:23:00 | 11/11/14 21:15:12 | 13/11/14 04:33:08 | 13/11/14 09:33:08 | 14/11/14 05:10:18 | OK | 14/11/14 12:00:00 |
| 14000892100 | 2 | 06/11/14 09:23:00 | 12/11/14 09:34:29 | 14/11/14 00:06:25 | 14/11/14 08:01:15 | 17/11/14 09:44:16 | 1 miss rs3736782 | 17/11/14 10:30:00 |
| 14000938200 | 3 | 06/11/14 09:23:00 | 12/11/14 13:58:50 | 13/11/14 17:30:52 | 14/11/14 08:03:22 | 15/11/14 09:56:33 | OK | 17/11/14 10:30:00 |
| 14000481803 | 1 | 06/11/14 09:23:00 | 13/11/14 04:33:09 | 14/11/14 09:42:54 | 14/11/14 12:35:00 | 15/11/14 12:42:20 | OK | 17/11/14 10:30:00 |
| 14000948900 | 3 | 06/11/14 09:23:00 | 13/11/14 17:30:53 | 15/11/14 01:04:53 | 16/11/14 13:03:00 | 17/11/14 08:42:31 | OK | 17/11/14 10:30:00 |
| 14000893600 | 2 | 06/11/14 09:23:00 | 14/11/14 00:06:26 | 15/11/14 08:51:57 | 16/11/14 13:05:06 | 17/11/14 08:36:20 | OK | 17/11/14 10:30:00 |
| 14000552800 | 1 | 06/11/14 09:23:00 | 14/11/14 09:42:54 | 15/11/14 18:52:37 | 16/11/14 13:03:00 | 17/11/14 09:15:13 | OK | 17/11/14 10:30:00 |
| 14000599400 | 1 | 06/11/14 09:23:00 | 15/11/14 18:52:37 | 17/11/14 03:43:24 | 17/11/14 08:28:24 | 18/11/14 04:24:12 | OK | 19/11/14 09:51:00 |
| 14000818200d | 1 | 06/11/14 09:23:00 | 16/11/14 13:28:04 | 18/11/14 05:05:26 | 19/11/14 08:51:00 | 20/11/14 11:46:52 | OK | 20/11/14 12:00:00 |
| 14000905700 | 2 | 06/11/14 09:23:00 | 15/11/14 08:51:58 | 16/11/14 12:24:21 | 16/11/14 13:06:54 | 17/11/14 10:58:12 | OK | 19/11/14 09:51:00 |
| 14000906400 | 2 | 06/11/14 09:23:00 | 16/11/14 12:24:22 | 17/11/14 18:50:56 | 19/11/14 08:51:00 | 20/11/14 04:31:28 | OK | 20/11/14 12:00:00 |
| 14000970401 | 3 | 06/11/14 09:23:00 | 15/11/14 01:04:53 | 16/11/14 04:21:58 | 16/11/14 13:06:54 | 17/11/14 09:29:33 | OK | 17/11/14 10:30:00 |
bold started underlined finished
| mapping 1 | mapping2 | mapping3 |
|---|---|---|
| 13000312105 | 14000874700 | 14000912100 |
| 13000343602 | 14000881700 | 14000912600 |
| 13001128402 | 14000882400 | 14000913100 |
| 14000176900 | 14000886003 | 14000918100 |
| 14000481803 | 14000892100 | 14000938200 |
| 14000552800 | 14000893600 | 14000948900 |
| 14000599400 | 14000905700 | 14000970401 |
| 14000818200d | 14000906400 |
Bad quality on the base starting around 115 for all samples
11.11.2014
mv Sample_Diag-excap33-14000874700-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../EEogPU/ mv Sample_Diag-excap33-14000881700-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../EEogPU/ mv Sample_Diag-excap33-13000312105-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../EEogPU/ mv Sample_Diag-excap33-14000912600-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../Bindevev/
12.11.2014
913 11/11/14 13:31:33 mv Sample_Diag-excap33-14000881700-EEogPU-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../EEogPU/ 918 11/11/14 13:36:39 mv Sample_Diag-excap33-13000312105-EEogPU-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../EEogPU/ 921 11/11/14 13:42:06 mv Sample_Diag-excap33-14000912600-Bindevev-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../Bindevev/ 922 12/11/14 08:48:42 mv Sample_Diag-excap33-14000882400-EEogPU-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../EEogPU/ 926 12/11/14 08:53:01 mv Sample_Diag-excap33-14000912100-EEogPU-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../EEogPU/ 927 12/11/14 08:53:23 mv Sample_Diag-excap33-14000913100-Bindevev-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../Bindevev/ 930 12/11/14 15:33:49 mv Sample_Diag-excap33-13000343602-EEogPU-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../EEogPU/
17.11.2014
1093 17/11/14 10:21:58 mv ToBePostProcess/Sample_Diag-excap33-14000481803-Ciliopati-v02-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../samples/Ciliopati/ 1094 17/11/14 10:23:04 mv ToBePostProcess/Sample_Diag-excap33-14000893600-Ciliopati-v02-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../samples/Ciliopati/ 1095 17/11/14 10:24:57 mv ToBePostProcess/Sample_Diag-excap33-14000552800-Bindevev-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../samples/Bindevev/ 1096 17/11/14 10:27:41 mv ToBePostProcess/Sample_Diag-excap33-14000948900-PCD-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../samples/PCD/ 1097 17/11/14 10:27:57 mv ToBePostProcess/Sample_Diag-excap33-14000970401-PCD-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../samples/PCD/ 1098 17/11/14 10:28:19 mv ToBePostProcess/Sample_Diag-excap33-14000892100-EEogPU-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../samples/EEogPU/ 1099 17/11/14 10:28:31 mv ToBePostProcess/Sample_Diag-excap33-14000938200-EEogPU-v01-KIT-Av5.141028_7001448_0280_BC5MRDANXX ../../samples/EEogPU/
Sample: Sample_Diag-excap33-13000312105-v01-KIT-Av5
Use as test to see if the new fingerprinting scripts work. Copy across the Home/workspace/amg/fingerprinting to diagInternal/diagnosticBundle/script/amg_test/fingerprinting
error in pipeline
Start to refine HGMD annotation ----- Tue Nov 11 08:08:43 CET 2014
Start to add HGVS intronic position ----- Tue Nov 11 08:08:43 CET 2014
Traceback (most recent call last):
File "/data/diag/diagInternal/diagnosticBundle/script/amg_test/annotation/pipeline/add_hgvs.py", line 26, in
from annotation.util.posconverter import posconverter
File "/data/diag/diagInternal/diagnosticBundle/script/amg_test/annotation/util/posconverter/posconverter.py", line 233
return iStart <= pos = iEnd
^
SyntaxError: invalid syntax
Start to add in-house db frequency and find the right transcript ----- Tue Nov 11 08:08:43 CET 2014
sample: Sample_Diag-excap33-14000912100-v01-KIT-Av5
error in 030_calculateHsMetrics
########### Evaluate alignment, insertion size and coverage ..... Checking which steps have been done ...... The 010_collectAlignmentSummaryMetrics need to be performed The 020_collectInsertSizeMetricss need to be performed The 030_calculateHsMetrics need to be performed The 040_coverageIn-house need to be performed Current work directory: /data/diag/diagInternal/samples/141028_7001448.B.Project_Diag-excap33-2014-10-24/Sample_Diag-excap33-14000912100-v01-KIT-Av5/030_postAlignQC Doing collectAlignmentSummaryMetrics ... start at ----- Mon Nov 10 20:00:22 CET 2014 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. (END)
First try to rerun it.
time vari /data/diag/diagInternal/samples/141028_7001448.B.Project_Diag-excap33-2014-10-24/Sample_Diag-excap33-14000912100-v01-KIT-Av5/data/sample.conf &> Sample_Diag-excap33-14000912100-v01-KIT-Av5bis.log
Sample : Sample_Diag-excap33-14000892100-EEogPU-v01-KIT-Av5
#################### 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.
Rerun it
yvans@loki:/data/diag/diagInternal/samples/141028_7001448.B.Project_Diag-excap33-2014-10-24/Sample_Diag-excap33-14000892100-EEogPU-v01-KIT-Av5 > time vari /data/diag/diagInternal/samples/141028_7001448.B.Project_Diag-excap33-2014-10-24/Sample_Diag-excap33-14000892100-EEogPU-v01-KIT-Av5/data/sample.conf &> Sample_Diag-excap33-14000892100-EEogPU-v01-KIT-Av5bis.log
Start novoalign for last sample
yvans@loki:/data/diag/diagInternal/samples/141028_7001448.B.Project_Diag-excap33-2014-10-24 > bash Sample_Diag-excap33-14000818200d-EEogPU-v01-KIT-Av5/data/commandMappingLoki.bash &> errcommandMappingLoki14000818200d.log