For seqware production, need to monitor the process report/fix errors accordingly.
Two important page:
11042010
A. It seems that Brian has cleaned up the errors, thanks!!
1. No event has happened to “101028_UNC2-RDR300275_00040_FC_62E9AAXX” yet
2. Only three successes with “101027_UNC7-RDR3001641_00050_FC_62J8EAAXX”, what is going on?
3. Hold on a minute, Brian corrected (deleted) the error, but did NOT fix the problem. Those missing files need to be re-stored!!
B. There was a problem (linking the file). For flowcell: 101022_UNC7-RDR3001641_00049_FC_62J92AAXX
1. 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.vendorQCsummary.txt exists on FS, but when click from LIMS, it fails
2. Detail output files like following:
/datastore/nextgenout/seqware-analysis/illumina/101022_UNC7-RDR3001641_00049_FC_62J92AAXX/seqware-0.7.0_RNASeqAlignmentBWA-0.7.4/seqware-0.7.0_BWA-0.7.0
[jyli@lbg-compute seqware-0.7.0_BWA-0.7.0]$ ls -tral 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.*
-rw-r—– 1 seqware nextgenseq 154 2010-11-02 02:33 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.uniqRead.txt
-rw-r—– 1 seqware nextgenseq 7494 2010-11-02 02:33 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.stat.txt
-rw-r—– 1 seqware nextgenseq 139 2010-11-02 02:33 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.qualFilter.txt
-rw-r—– 1 seqware nextgenseq 478 2010-11-02 02:33 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.vendorQCsummary.txt
-rw-r—– 1 seqware nextgenseq 65 2010-11-02 02:33 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.adapterCont.txt
-rw-r—– 1 seqware nextgenseq 1781 2010-11-02 02:33 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.trimmed.txt
-rw-r—– 1 seqware nextgenseq 405 2010-11-02 02:33 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.stat.summary.txt
-rw-r—– 1 seqware nextgenseq 6327810056 2010-11-02 02:47 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.trimmed.fastq
-rw-r—– 1 seqware nextgenseq 14187 2010-11-02 03:46 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.bxp.png
-rw-r—– 1 seqware nextgenseq 13962 2010-11-02 03:46 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.BCtrend.png
-rw-r—– 1 seqware nextgenseq 366 2010-11-02 03:46 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.BCtrend.txt
-rw-r—– 1 seqware nextgenseq 15 2010-11-02 03:46 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.BCflag.txt
-rw-r—– 1 seqware nextgenseq 344 2010-11-02 03:46 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.qcGenome.txt
-rw-r—– 1 seqware nextgenseq 298 2010-11-02 03:46 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.GenericQCGenome.txt
-rw-r—– 1 seqware nextgenseq 11917 2010-11-02 03:46 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.ntDistr.png
-rw-r—– 1 seqware nextgenseq 2013317829 2010-11-02 03:49 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.trimmed.raw.bam
-rw-r—– 1 seqware nextgenseq 2068081081 2010-11-02 04:36 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.trimmed.annotated.bam
-rw-r—– 1 seqware nextgenseq 9765 2010-11-02 07:34 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.TRcov.png
-rw-r—– 1 seqware nextgenseq 972296 2010-11-02 07:34 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.trimmed.annotated.gene.quantification.txt
-rw-r—– 1 seqware nextgenseq 2003 2010-11-02 07:34 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.TRcov.txt
-rw-r—– 1 seqware nextgenseq 315 2010-11-02 07:34 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.alignStat.txt
-rw-r—– 1 seqware nextgenseq 3343555 2010-11-02 07:34 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.trimmed.annotated.transcript.quantification.txt
-rw-r—– 1 seqware nextgenseq 2060617606 2010-11-02 07:36 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.trimmed.annotated.translated_to_genomic.bam
-rw-r—– 1 seqware nextgenseq 8458 2010-11-02 08:47 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.geneCoverage.png
-rw-r—– 1 seqware nextgenseq 811 2010-11-02 08:47 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.geneCoverage.txt
-rw-r—– 1 seqware nextgenseq 8950203 2010-11-02 08:47 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.trimmed.annotated.spljxn.quantification.txt
-rw-r—– 1 seqware nextgenseq 13842696 2010-11-02 08:47 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.trimmed.annotated.exon.quantification.txt
-rw-r—– 1 seqware nextgenseq 70608115 2010-11-02 08:47 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.bigwig
C. As of today, 11042010, how does QC do? Using 101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1 as an example
1. IllQualStat (success):
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.vendorQCsummary.txt
2. BCtrend (success):
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.BCtrend.png
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.BCtrend.txt
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.BCflag.txt
3. qualStat (success):
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.stat.txt
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.stat.summary.txt
4. uniqRead (success):
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.uniqRead.txt
5. adapter/TrimCountAdapt(success):
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.adapterCont.txt
6. qualFilter (success):
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.adapterCont.txt
7. qcGenome (success):
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.qcGenome.txt
8. alignStat (success):
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.alignStat.txt
9. geneCoverage (success):
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.geneCoverage.txt
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.geneCoverage.png
10. plotStats (success):
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.bxp.png
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.ntDistr.png
11.coverageXTranscript (success):
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.TRcov.txt
101022_UNC7-RDR3001641_00049_FC_62J92AAXX.1.TRcov.png
11052010
1. Helped Alicia to get her data
2. For IllQualStat
3. For BCtrend
