ContamCheck not working?

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I was looking at a number of recent WGBS libraries that all seem to have N/A 
for all the "q0" contamCheck metrics.  I went to look at the ContamCheck 
flagstat files and they all seemed to have 0 reads.  I'm not sure if the 
pipeline alignments are working properly and have 0 mapped reads, or if the 
pipeline part is just not working.  If it's working properly, the ECDP should 
show 0% rather than N/A.  But I have a feeling the pipeline is not running 
correctly for these.  Did we turn it off on purpose?

Original issue reported on code.google.com by benb...@gmail.com on 9 Nov 2012 at 10:06

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Original comment by benb...@gmail.com on 9 Nov 2012 at 10:07

Attachments:

• Untitled.png

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checked multiple runs, the pipeline and workflows are generating this correctly.

But is not being parsed/pulled/displayeed into the db/ecdp correctly.  

[ramjan@hpc-uec C18FYACXX_1_NIS1509A10]$ pwd
/export/uec-gs1/laird/shared/production/ga/flowcells/C18FYACXX/results/C18FYACXX
/C18FYACXX_1_NIS1509A10
[ramjan@hpc-uec C18FYACXX_1_NIS1509A10]$ cat ContamCheck.*
0 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
0 + 0 mapped (nan%:nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (nan%:nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (nan%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
5000000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
166177 + 0 mapped (3.32%:nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (nan%:nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (nan%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
5000000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
3035485 + 0 mapped (60.71%:nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (nan%:nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (nan%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
0 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
0 + 0 mapped (nan%:nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (nan%:nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (nan%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
5000000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
0 + 0 mapped (0.00%:nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (nan%:nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (nan%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
0 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
0 + 0 mapped (nan%:nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (nan%:nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (nan%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
5000000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
2519 + 0 mapped (0.05%:nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (nan%:nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (nan%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
0 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
0 + 0 mapped (nan%:nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (nan%:nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (nan%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

Original comment by zack...@gmail.com on 10 Nov 2012 at 1:45

• Changed state: Started
• Added labels: Project-NGS-ECCP

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this is some very old code that I'm familiar with and needs to be redone.  
as samtools output format changed at the end of last year, this broke.

I'll take this one.

Original comment by zack...@gmail.com on 12 Nov 2012 at 9:10

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in addition, found some broken pipeline stuff that needs to be fixed in 
workflows

Original comment by zack...@gmail.com on 12 Nov 2012 at 10:19

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Issue 346 has been merged into this issue.

Original comment by zack...@gmail.com on 13 Nov 2012 at 8:15

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Issue 157 has been merged into this issue.

Original comment by zack...@gmail.com on 14 Dec 2012 at 5:05

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fixed.

Original comment by zack...@gmail.com on 14 Dec 2012 at 5:05

• Changed state: Fixed