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Recent Activity
phage that crash starterator
| Link to this post | posted 08 Feb, 2017 21:42 | |
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Ok well it appears that flaverint does not crash my current "development" version of Starterator. So I can generate a whole phage report using it. The problem with the development version is that I have taken out much of the code that generates the summary text below the graph in anticipation of adding improved versions along the lines of the improvements to the single pham reports. Consequently the whole phage report that comes out has all the graphics but none of the summary text. So, no counting which starts are annotated and/or conserved and no list of base locations for the various starts in the phage being analyzed, this means the online version is still better for all that info. The good news is that these whole phage reports do have the part of the PDF that you need to upload to PECAAN and PECAAN will have the links to the online versions. Below are links to download the whole phage report for the crashing phage mentioned above as generated by the development version of starterator (for anyone interested the current development version is this branch of my person github repo). Whole phage pdf report for Aggie using development version of Starterator Whole phage pdf report for Flaverint using development version of Starterator Whole phage pdf report for Mattes using development version of Starterator Whole phage pdf report for Andies using development version of Starterator Whole phage pdf report for Philonius using development version of Starterator Whole phage pdf report for Aroostook using development version of Starterator |
| Link to this post | posted 08 Feb, 2017 22:55 | |
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cdshafferCHRIS!!!!! YOU ARE AWESOME!!!! Thank you so much!!!! gf   
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| Link to this post | posted 26 Feb, 2017 15:37 | |
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cdshaffer Thanks so much Chris! I have a question related to this. The pham number in this report (for Mattes) does not always match that on the phamerator map. If the students use this starterator data download for their annotation, should I be worried about these discrepancies? |
| Link to this post | posted 27 Feb, 2017 05:41 | |
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I would need specific examples to know for sure but the pham numbers do change sometimes as new proteins are added. Right now the with all the new phages, Travis is posting 2 updatess to the database each week. So, it depends on where you get your map, how old the map is, and when the starterator report was generated. It is quite possible the two are out of sync. This is the reason that we decided to add the date on the starterator report, the older the report the more likely the discrepancy is due to the numbers changing with the new phages being added. I am trying to keep the online starterator reports here as up to date as I can. So far I have been able to get everything posted within 1 working day of when the new database is posted. So the online starterator reports should be (mostly) in sync with the info at phagesdb.org. If you want to double check a discrepancy you can always check the pham at phagesdb.org; the page on the pham will list all the current proteins based on the most recent database release, you can then compare that to the most recent map by using the SEA VM, start phamerator and make sure it completes an full update before creating the map (this can take quite a while depending on your set up). I am not sure for the online version of phamerator how often it gets updated but it does tend to lag behind a bit. Hope that helps, if you are still not sure post an example or two and I would be happy to double check that it is not a more serious coding error. |
| Link to this post | posted 27 Feb, 2017 10:53 | |
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Thanks Chris. I checked on phages.db and the phams listed in your starterator report for Mattes are correct (For example, pham 25681 on the starterator report was given as 24343 on phamerator). I will check for a full update on phamerator to see if this issue is resolved. |
| Link to this post | posted 13 Apr, 2017 20:15 | |
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Phage chance64_draft crashes at 58 of 59. I have tried to run it multiple times on two different computers. I have seen in other posts that you have been kind enough to run the "reticent" phages. I would be most grateful if you could find the time to run Chance64_draft. Thanks for any help you can give. Marsha |
| Link to this post | posted 13 Apr, 2017 21:15 | |
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Marsha, Happy to help. It's too bad all the updates I wrote last fall were too late for inclusion in the SEA VM for 2017. The good news is that its fairly easy for me to set up a run on a whole phage, the computer does all the hard work anyway. You can get the full report from this link. The output is different that what is produced with the older version. The report now focus on the human annotated genes more and the auto-annotations less. I hope you find it useful. |
| Link to this post | posted 13 Apr, 2017 22:04 | |
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Thank you so much Chris! It has not been a good month for me and the phage programs. I am dealing with a rash of crashing DNA Master programs and files and the Starterator problem was almost the one that would have put me over the edge. We owe you big time! Marsha |
| Link to this post | posted 04 May, 2017 22:37 | |
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Thank you for all of your suggestions! We're on the current database (for both Phamerator and Starterator) and we've deleted all of the intermediate files. We are working on DismalFunk and Starterator works great until it gets to pham 85 (out of 95), and then it crashes. Any help would be greatly appreciated and thanks! Kathleen |
| Link to this post | posted 08 May, 2017 19:13 | |
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Sorry this took so long. I was so buried with grading final reports I did not have time to check the forums until today. Here is your DismalFund starterator report It is in the standard format, there is also a new experimental output (See this discussion for example). If you would like the report in that forma let me know, it is trivial easy to rerun. |