SEA-PHAGES | Trouble with phage Hegedechwinu

Link to this post \| posted 13 Feb, 2018 17:54
cdshaffer	I am cross-posting this request for starterator help from grosasacosta below: I am having issues with Starterator. I've been trying to run it for Hegedechwinu but it keeps crashing when it reaches Pham 92 (near the end of the analysis). Any suggestion on how to solve this issue? It is related to that specific Pham. From what I saw in other similar posts, the solution may not be simple at all. Please let me know if you have any suggestions on how to solve this issue, I will be waiting. Edited 13 Feb, 2018 18:04

Link to this post | posted 13 Feb, 2018 17:54

I am cross-posting this request for starterator help from grosasacosta below:

I am having issues with Starterator. I've been trying to run it for Hegedechwinu but it keeps crashing when it reaches Pham 92 (near the end of the analysis). Any suggestion on how to solve this issue? It is related to that specific Pham. From what I saw in other similar posts, the solution may not be simple at all. Please let me know if you have any suggestions on how to solve this issue, I will be waiting.

Edited 13 Feb, 2018 18:04

Link to this post \| posted 13 Feb, 2018 18:24
cdshaffer	Unfortunately the last build of the SEA VM was done before I was able to release the version of Starterator with all the bug fixes. So the SEA VM version will work for many but not all phage. I have run a full phage report for Hegedechwinu on the updated version of starterator and you can download it from here: https://wustl.box.com/s/16md6n7clzkwz13xdvfpabxu8c28gjp5 Feel free to download and use. Be aware that what might work better for you is to use the pre-computed starterator reports. The nice thing about these reports is they are automatically updated with each new release of the phamerator database. These pre-computed pages are part of the effort to get away from the VM and get as much as possible available via web browser. These reports are available as links off of the phagesdb pages for the phams and the individual gene pages. Examples for pham 431: http://phagesdb.org/phams/431/ (Pham page, click on the blue “Get Starterator Report” button at the top of the page.) Example for gene 9 of phage Pollywog: http://phagesdb.org/genes/POLLYWOG_DRAFT_9/ (Gene page, click on the link “Pham 431 Report”, fourth row of the table.) Alternative methods for obtaining the reports are discussed on this forum page well. Edited 14 Feb, 2018 01:31

Link to this post | posted 13 Feb, 2018 18:24

cdshaffer

Unfortunately the last build of the SEA VM was done before I was able to release the version of Starterator with all the bug fixes. So the SEA VM version will work for many but not all phage.
I have run a full phage report for Hegedechwinu on the updated version of starterator and you can download it from here:

https://wustl.box.com/s/16md6n7clzkwz13xdvfpabxu8c28gjp5

Feel free to download and use. Be aware that what might work better for you is to use the pre-computed starterator reports. The nice thing about these reports is they are automatically updated with each new release of the phamerator database. These pre-computed pages are part of the effort to get away from the VM and get as much as possible available via web browser. These reports are available as links off of the phagesdb pages for the phams and the individual gene pages.

Examples for pham 431:
http://phagesdb.org/phams/431/
(Pham page, click on the blue “Get Starterator Report” button at the top of the page.)

Example for gene 9 of phage Pollywog:
http://phagesdb.org/genes/POLLYWOG_DRAFT_9/
(Gene page, click on the link “Pham 431 Report”, fourth row of the table.)

Alternative methods for obtaining the reports are discussed on this forum page well.

Edited 14 Feb, 2018 01:31

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Trouble with phage Hegedechwinu