[sagarutturkar]

Hi,

I recently upgraded to version 2.0 of SmartPortal. When I go to design new job, I see 3 SMRt cells available with different ID. Is there any way, I could delete this SMRT cells and re-import again as fresh?

My role is 'Scientist' and assigned to group 'all'.

Also, when I tried to run this with test data as mentioned at :

https://github.com/PacificBioscience...tallation-v2.0I got the error given in log file.

Please help with this.

Thanks
Sagar

Thanks
Sagar

[sagarutturkar]

Attached log file here.

[GenoMax]

rhall provided an important pointer about SMRTanalysis v.2.0 which got our install of SMRTportal going with HGAP protocol.

The critical pointer was to make sure that the cluster nodes were also set up as submit hosts. I do not think that is explicitly mentioned in the install materials (at least it was not before).

[rhall]

Sagar, can you try posting the log file again?
Thanks.

[sagarutturkar]

Hi rhall,

Thanks for your reply and providing the data. I am able to run the SMRTportal 2.0 now. I was able to run the HGAP and AHA. For our small Microbial Genomes, I have 1 SMRTcell sequenced which is around 25x coverage.

Genome 1 - CF80
The AHA and HGAP failed, Log attached. I was able to run the AHA through command line (v 1.4) using same files (I used fastX toolkit to convert filtered_subreads.fastq file to fasta format and used existing assembly as reference.)

Genome 2 - BT
I was able to run the HGAp. But the expected genome size was 11 MB and my assembly size is pretty small. What could be done to improve this.

Logs attached.

Thanks
Sagar

[rhall]

CF80, how old is this data? The long_ and strobe_ bas.h5 files do not contain any data, and as far as I know where never generate by the PacBio RS. Try removing these files and trying again.

BT, HGAP requires a minimum of ~70x of raw read coverage to assembly a complete genome. A rough calculation, I would estimate that you would need ~8 cells of data (with long insert size) to get a good assembly. On the new RSII this would be fewer, but still dependent on the library size.

Also note, you set an expected genome size of 5MB in the HGAp run.
SMRT portal has a limit of 10MB for HGAP assemblies, it is possible to assembly up to 130MB using the command line SMRT Pipe.