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Greetings, we started the assembly of a small bacterial genome from 1 SMRT PacBio run last night on Amazon EC2 services using HGAP. Just wondering if anyone else out there has tried this, and could provide a time estimate for assembly. There were 87000 post-filtered post filter polymerase read length ~4700bp. The tutorial I watched used optimized E. coli reads with several SMRT cells on a multi-CPU computer, they said it would take ~few hours...
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What size instance are you using? are you using the HGAP.1, or HGAP.2 protocol? Viewing the log, top right on the job page will give you a % complete estimate. Also viewing ./common/userdate/jobs/<job id>/workflow/Workflow.summary.html will give you a detailed view of the tasks that have complete, and what is remaining to be ran.
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