I'm trying to assemble a bacterial genome (about 4.1Mbases in length) using HGAP in smrtanalysis 2.0.1. The job runs until the draft assembly is finished and then fails after that point. I am at a loss as to how to fix this problem. I am running this on a single node machine. I have attached the master.log and smrtpipe.log files. I would really appreciate any help I can get with this matter.
I should mention that I've run HGAP on the included lambda SMRT cell and it does get all the way to a polished genome, so it seems to me that I have smrtanalysis set up correctly on my system.
I should mention that I've run HGAP on the included lambda SMRT cell and it does get all the way to a polished genome, so it seems to me that I have smrtanalysis set up correctly on my system.
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