Importing Illumina data onto SMRT portal

[tonybert]

Greetings, I have been trying to run the celera assembler using STAR-cluster on amazon-EC2 on some PacBio long reads (1 smrt cell) and paired end Illumina data (100 bp PE). The genomes we are trying to assemble are ~1.6-2.0 Mbp. I am 99% sure I have installed the assembler correctly, as I was able to perform one of the example/tutorial assemblies of a small virus (A006, 35kbp mock genome). I have been able produce the .frg files for the Illumina data, and I have filtered_subreads.fastq from the sequencing center. However, when I run ./pacBioToCA I keep getting errors that I believe have something to do with SGE conditions (the full command/output is attached, command_line_output);

qsub: illegal -p value
qsub: illegal -c value ""

I was under the impression that these values would be defined in the pacbio.spec file (see attached), but they are not, and I am not sure how to modify these. I'm pretty new to the CeleraAssembler and running SGE jobs on STAR, so any comments/suggestions/hints are welcome. I

[rhall]

To add, the hybrid assembly support in SMRT Analysis was never great, I would not recommend going back to a previous version. Hybrid assembly as implemented in PBcR , ECTools, or dbg2olc is going to be much more straightforward and give better results.

[GenoMax]

Here is a post from Dr. Hall who works at PacBio from the thread I linked above: http://seqanswers.com/forums/showpos...46&postcount=5

Hybrid assembly is no longer supported in SMRTportal v.2.3. You may have to install/use an older version of SMRTportal if you want to use hybrid assembly.

[tonybert]

Yes, all the xml, .bas.h5, .bax.h5 files are all there. Its the short Illumina data that I'm trying to place, or figure out where to place within the context of the SMRT Portal. I can run HGAP on the smrt-cells, but we really want to do a hybrid assebly. I can navigate to the Manage and Import section, select managed protocols and select the RS_CeleraAssembler. I then copy this, and save as RS_CeleraAssemblerModified. In the Protocol Preset Details the FASTQ to Correct with is Empty. I have tried entering the name of the Fastq file that I have uploaded to /opt/smrtanalysis/common/references_dropbox, but it will not recognize this file. So, i am guessing that the path it is looking for is different than this. I'll look back at the git-hub post again. Thanks.

[GenoMax]

Do you have original data for the SMRTcell(s) you are trying to import?

Here is a list of minimal files you need (*.metadata.xml file and all *.bax.h5 and *.bas.h5): https://github.com/PacificBioscience...to-SMRT-Portal

BTW: See this if you are specifically looking for CeleraAssembler. http://seqanswers.com/forums/showthread.php?t=49846

[tonybert]

Greetings, I am trying to run the RS_Celera assembler on the SMRT Portal. I have set this up the "easy" way using amazon cloud computing. I am able to move the PacBio data onto the cloud. However, I am not able to get the Illumina data on. However, I am not entirely sure where it should go. I have tried placing it in the reference sequence files (although they are not "reference genomes"), but this fails. Any suggestions are useful.