Unable to get Mapping graphs in SMRTportal

[sagarutturkar]

Hi,

I have SMRTportal version 2.2 installed. I am running HGAP_3 protocol with my data which completes without any problems. However, somehow when i click on Mapping section, All graphs appear to be empty. All other graphs, e.g. adapters, subread filtering, coverage, corrections are there. But mapping graphs appear empty.

I tried this workflow with lambda test genome and it generates mapping graph correctly. I therefore recognize something wrong with data files, and reloaded data from backup. Still having same issue.

One thing I noticed is in report, the correct graphs mention SMRTcell IDs as "m130....." while failed mapping section mentiones IDs as "XSBOR...". I am not sure where it is picking wrong name/IDs and workaround for this.

This is very weired, but very frustrating to figure out.

PDF report attached. Any help is much appreciated.

Thanks
Sagar

[GenoMax]

Create a ticket with PacBio tech support. They may need to see log files etc in order to diagnose this. Looks like you have not upgraded to 2.3 yet.

[sagarutturkar]

Hi Genomax,

Thank you for your reply. I upgraded to version 2.3, but having some issues to run HGAP job with same data. I opened an issue on pacbio github here:

https://github.com/PacificBiosciences/SMRT-Analysis/issues/164#issuecomment-69061474

However, it was not solved for more than a week and I had to revert to version 2.2 which is atleast able to finish the HGAP job. For PacBio tech support, Github is the best place or do you have any other specific forum/email where issue could be reported?

Thanks
Sagar

[GenoMax]

Sagar: Email the address on this page (http://www.pacificbiosciences.com/support/).

If you have access to PacBio Portal you can log a case from there. Portal way is likely better.

[sagarutturkar]

GenoMax,

Thanks for your reply. I have contacted support as well as post this on github at:

https://github.com/PacificBiosciences/SMRT-Analysis/issues/166#issuecomment-69964287

Hopefully it will be resolved.

Thanks
Sagar

[rhall]

This is getting solved in other forums, but it looks like the root cause is the renaming of primary data. It is not possible to rename primary files, parts of the pipeline require the names to match those reference internally in the bax.h5 files. The files should be named to match the root of the read name m130...

[sagarutturkar]

Hi rhall,

Thanks for your reply. This is how my data structure looks like:

This is how my directory structure looks like.

Data looks like:
DSM10061
XSBOR_20130726_RS42150_PL100036291-1_C02.metadata.xml
XSBOR_20130726_RS42150_PL100036291-1_D02.metadata.xml

Analysis_Results
XSBOR_20130726_RS42150_PL100036291-1_C02.1.bas.h5
XSBOR_20130726_RS42150_PL100036291-1_D02.1.bas.h5
XSBOR_20130726_RS42150_PL100036291-1_C02.1.1.bax.h5
XSBOR_20130726_RS42150_PL100036291-1_C02.1.2.bax.h5
XSBOR_20130726_RS42150_PL100036291-1_C02.1.3.bax.h5
XSBOR_20130726_RS42150_PL100036291-1_D02.1.1.bax.h5
XSBOR_20130726_RS42150_PL100036291-1_D02.1.2.bax.h5
XSBOR_20130726_RS42150_PL100036291-1_D02.1.3.bax.h5

I believe I have ran this through previous version of SMRTanalysis with same files names and I got correct results. The previous report shared at:

https://www.dropbox.com/s/ubt6u8xwbe43f94/DSM10061_HGAP_Report.pdf?dl=0

Do you think I should rename all the data files (including bax.h5, bas.h5) with basenames "m130727_043304_42150_c100538232550000001823086511101337" and "m130727_021351_42150_c100538232550000001823086511101336". I just wanted to confirm your opinion before proceeding.

Thanks
Sagar

[sagarutturkar]

Well, I did this. renamed all the files with "m130....". But somehow, no luck.
The mapping report shows different names now, but still no graphs appear.

New report shared at: https://www.dropbox.com/s/6h2l0cjix0..._try2.pdf?dl=0

Hopefully somebody can help.

[sagarutturkar]

Solved

This is solved by PacBio and instructions are available at:

https://github.com/PacificBiosciences/SMRT-Analysis/wiki/Cannot-import-new-SMRT-Cells

Thanks
Sagar