We just submitted our assembly job, and in this video we're going to talk about monitoring the job progress, and looking at the results. So the job has been submitted, it says here it's been queued, how do I find information about that job? My favorite place to go is to this jobs monitor down at the bottom, and click on that, and it takes me to My Jobs page. You can also get to there from going to Workspace to My Jobs, now you can see that this genome assembly that we just submitted, is currently running. But if we want to look at a job that that we've had success running, I'll narrow down mountain because I have a lot of data in my workspace, and under this all services I'll click on the down arrow and click on Genome Assembly 2, there's the job that's running. But this is a recently completed assembly job, so let's look at what it looks like when that job is complete. So I select this row, and notice that as soon as I select the row, some information appears in this vertical green bar, it shows me how I can view the job or report an issue, if you have a failed assembly job, we want to know about it, so you need to do that, but this job completed successfully. So let's click on view results, so in this upper box it gives us the information about the assembly job, how long it took to run, when it started, and if I click on the Parameters box, it's going to show me the data that I submitted and information about that job. But the main thing you want to look at here, are these things, the Assembly report and this is the context file. Things are the assembled context, and then we'll talk a little bit more in detail about this particular folder with details, but the most valuable thing to me right now is this assembly report, so let's click on that. And then we can click on View, and this takes us to the genome Assembly report, and gives me information about it. It tells me what reads I put in for that particular job, what assembler it shows, how long the job took, more information about the contact, fast a size, the command line, it also provides a Quast Report. Here quast record as a quality assessment tool for evaluating and comparing genome assembly, and you can dig into details, it provides you with a lot of different tables and figures that you can match through to look at how good your assembly is. One of the main things you want to see is how many context you had, how many context of each size, the total length of the genome, so it gave us a total of 63 contig. Remember, we had selected the default was contig greater than 300 base pairs and, it tells you the largest contig and the total size. And these are figures that you could put directly into a publication when you're describing the assembly, it's telling you if it did any post assembly transformations on this, per pylon, if it did any trimming, it's looking at the contig filtering. How many contigs were above the thresholds? All 63 contigs were above both the minimum contig length, and the coverage threshold, and it also gives you, I mean, I don't know how useful this is, but I really like looking at the bandage plot. So it's showing you what the Assembly looks like, and how it all went together, and I like that a lot. To get back to the information about the job, we've got this bread crumb across the top so I can click here, this will show me the contig's file now this contig's file is already ready to be annotated and Patrick, so you would see it directly in the annotation service. because as you can see, it's correctly tagged, if you wanted to download the contig's file and see what it looks like, that's where the general contig's file looks like, let me open this up a bit so you can see it more. It shows you the name of the strain, gives me the number of the contig, tells you how long that contig is, and what the coverage and the normalized coverage score Rs. That's generally how we reported in Patrick is on a contig by contig basis. And the sequence of course begins on the second row. Now if you need more information, we'd like to give you everything but we don't like to have a huge number of files in the immediate these are what I think are the two most valuable files, but you can also look on the details file, by clicking on this folder. And this shows you all the different data that you can get the Assembly graph, which is that bandage plot, you can get it in two different formats, this is the computer logs about the Assembly. These are different versions of the Quast report that you can look at the transpose Quast report, and we also provided JSON file. Now JSON file is a file that stores simple data structures and objects in JavaScript object notation, which stands for JSON, and it's the standard data interchange format. It's primarily used for transmitting data between the web application and a server. This isn't recommended for you to view, it's for a computer to view, but it's here and you can look at it, and we also provide the unicycler log file for each time it's run. Once again, this isn't recommended for viewing, but it is downloadable and viewable, so this is the kind of information that's available with your assembly. And congratulations if you get to this point, you had a successful assembly, and so, you've learned how to upload files, how to load the reads, how to choose the correct parameters, which includes the correct recipe for assembly. Submitting the job, and then looking at the download files so the only thing left to talk to you about, is what to do when you have a problem and that will be in the next video, thanks.
