[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.

[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]

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

[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).

[sagarutturkar]

Attached log file here.

[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

[rhall]

Correct me if I'm wrong, are you trying to use SMRT Analysis with Solid sequence data? While some parts of SMRT Analysis may be able to handle Solid data, the workflow is really designed for PacBio data.
Trying to run the command in ./workflow/P_Filter/filter_001of001.sh should give you a more descriptive errror.

[juassis]

[QUOTE=rhall;98498]I work for PacBio, but not in tech support. If the installation is tied to a machine then go through your FAS for SMRT Analysis install support.

Cheers for your answer, it was very helpful.
But, I don't understand the error message generated, with solid datas.

Solid - library mate pair - reads = 2.159.990.294 - coverage 37x (151 GB)

error log message as below:

[ERROR] 2013-05-20 14:24:19,051 [pbpy.smrtpipe.engine.SmrtPipeWorkflow execute 602] task://Anonymous/P_Filter/filter_001of001 Failed
Traceback (most recent call last):
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtPipeWorkflow.py", line 600, in execute
raise WorkflowError(task.error)
WorkflowError: task://Anonymous/P_Filter/filter_001of001 Failed

[ERROR] 2013-05-20 14:24:21,218 [pbpy.smrtpipe.SmrtPipeMain run 648] SmrtExit task://Anonymous/P_Filter/filter_001of001 Failed
Traceback (most recent call last):
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/SmrtPipeMain.py", line 608, in run
self._runTasks(pModules)
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/SmrtPipeMain.py", line 281, in _runTasks
workflow.execute()
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtPipeWorkflow.py", line 605, in execute
raise SmrtExit(str(e))
SmrtExit: SmrtExit task://Anonymous/P_Filter/filter_001of001 Failed
[ERROR] 2013-05-20 14:24:21,238 [pbpy.smrtpipe.SmrtPipeMain exit 760] SmrtExit task://Anonymous/P_Filter/filter_001of001 Failed

---

thanks

[rhall]

For anyone still having issues with SMRT Analysis installations, I'm experimenting with a simpler, somewhat limited, install method using Vagrant and VirtualBox.

https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/SMRT-Analysis-2.0-Virtual-Machine-Install-(Experimental)

[GenoMax]

Then a separate big cluster is needed for secondary analysis, which is not the part of the package, correct?

Rhall has already explained the basics. You can download the secondary analysis software (both command line/web front end) here: http://pacbiodevnet.com/.

Note: Secondary analysis software is only supported on CentOS and Ubuntu (note the specific versions there in). Stepping outside those will likely prove an exercise in futility (i.e. do not try it, in most cases it does not work). If you are running a OS version that is not one of the two supported then consider using a virtual server.

[rhall]

Primary analysis, base calling, has always been done on the blade cluster, which is part of the instrument.
A separate cluster is needed for secondary analysis tasks, that is not part of the package that PacBio sells, the size of this depends on what you want to do and can range from a high end workstation to a 100 node cluster.

[yaximik]

Primary analysis is done on the machine, the data is then transferred off the machine for secondary.

I guess I was not clear. My understanding was that since beginning primary processing (base calling, etc.) was done somewhere at PacBio uusing their proprietary software. Correct me if I am wrong.

Now it seem all done localy, I mean on the instrument (primary) and off instrument, on some separate datarig (secondary).

It is mentioned that a blade cluster is the part of the instrument, I guess inside their big box, intended for primary processing. Then a separate big cluster is needed for secondary analysis, which is not the part of the package, correct?

I sent a info request to PacBio, hope their sales people get back to me and explain all that.

[rhall]

Primary analysis is done on the machine, the data is then transferred off the machine for secondary.

[yaximik]

After browsing through the PacBio site I got impression that now the system is self-contained, that is both primary and secondary analysis are done locally. Is that correct, or raw data are still uploaded for primary analysis to PacBio's server and then send back for secondary analysis done locally? That would make it quite dependable on network reliability and the transfer rate, which varies a lot on my local network.

[GenoMax]

I work for PacBio, but not in tech support. If the installation is tied to a machine then go through your FAS for SMRT Analysis install support.

That solves that mystery. You had very specific info that normal users do not (and we have had pacbio for a while).

Juassis: PacBio has a customer portal at: http://www.pacbioportal.com/. I am not sure if you need to have an instrument to get access. As rhall suggested you may need to go through your FAS.