[tonybert]

Hi GenoMax, the output from our PacBio sequencing facility consists of a directory that contains another directory (Analysis Results), filtered_subreads.fastq.gz, DS_Store, and a file with a .xml extension. Analysis results has all the .bax.h5 and .bas.h5 files. Would RS_subreads be something that would come off of the smrt portal?

I am in the "PacBio should be enough" camp but to be fair PacBio data tonybert has needs to be of good quality. The "sweet spot" for getting a good assembly appears to be library specific in our hands.

@tonybert: Can you post stats from a "RS_subreads" run for your SMRTcell?

[tonybert]

Hi GenoMax, this is from the smrt portal.
Mean Subread length 2,677 N50 3,055
Total Number of Bases 447,142,427 Number of Reads 166,982

I was trying to run HGAP.2, but it run never completed, it failed.

[rhall]

The subread length will be the limiting factor, but your coverage is sufficient for PacBio only assembly. You should be able to run HGAP.3 on the cloud instance of SMRT Analysis without using Star cluster, although it will require one of the larger computational instances.
For the HGAP.2 run, was that on a cloud instance? Do you have any logs, specific errors?

[tonybert]

Yes, see atttached, this is from the smrt analysis portal.

[tonybert]

If the subread length is ~2500, then I should probably decrease the minimum seed length, correct? The default is 6000. Could this be why its failing?

[rhall]

From the log that you posted, the seed length is being automatically set (based on 30x of reads for the input genome size), so the 6000 is ignored, although with a 2500 mean subread length it is possible that you will still have significant coverage of reads >6kb.
Can you check the output directory for the ./data/corrected.fasta file to make sure that the preassembly is working. Also if you could post the ./logs/P_CeleraAssembler/runCaHgap.log as that is the specific job that failed.