Link to this post | posted 12 Feb, 2020 23:30

cdshaffer

Just a reminder to everyone that the most recent updates to Starterator were designed to improve the whole phage reports. These whole phage reports steamline some of the output that is needed for a whole pham report but is irrelevant if all you care about is annotating one particular phage. Unfortunately I cannot pre-compute whole starterator reports, its just too computationally intensive, but I am happy to generate a whole phage report for anyone by request. Simply post a follow-up message to this post or send me an email. All I need is the name of the phage and I can generate a report based on the initial auto-annotation. Be aware that for phage in large clusters it can take several hours of computation so expect some delay between request and response but it only takes me about 45 seconds to start the run and another 75 seconds to post the results so don't feel like this is a huge ask, happy to help. Also, you may find it helpful to run a whole phage report on a phage after you have worked on annotation and want to rerun the whole phage report based on those newer annotations. I can do that easily as well. Simply email me either your DNA Master file, or if you are using PECAAN export and send me the "CDS function" report and I can run a whole phage starterator report based on that new annotation set. Edited 13 Feb, 2020 03:26

Link to this post | posted 08 Feb, 2020 00:29

cdshaffer

Yes there was a new version of the database posted this morning. Since each site updates as it can things can get out of sync. Not sure how you generated what you are calling your "gene list" but pecaan and phagesdb were updated earlier today so the links out of pecaan and out of phagesdb were pointing to pages that did not exist until starterator was also updated to the new version 339. This is how you can get the info on which version each site is on (links will only work between two sites if they are on the same version): phagesdb see: http://phamerator.webfactional.com/databases_Hatfull/Actino_Draft.version starterator see: http://phages.wustl.edu/starterator/database.version pecaan: look on any "pham maps" page just above the map phamerator.org: open the pull down menu in the top left Edited 08 Feb, 2020 00:30

Link to this post | posted 05 Feb, 2020 20:13
cdshaffer	I am adding an online link so it is much easier to see the current Starterator database version. This link should always give the most recent database version that has been published: http://phages.wustl.edu/starterator/database.version

Link to this post | posted 05 Feb, 2020 16:20

cdshaffer

Yes a typo of any kind can keep the system from changing to a green check. One simple error that is hard to detect is if there is a space character to the beginning or end of the function. The other thing worth mentioning but cannot explain your high rate is that the approved function list changes quite quickly but Pecaan only updates its list periodically. So again you can have synchronization issues. It is not uncommon for us to have an X or two by the end of an annotation because of this. Not sure why you are getting up to 1/3rd. So my suggestion is the same as JoAnn, encourage the students to type just a few characters in the function and then select the correct entry from the dropdown. Edited 05 Feb, 2020 16:26

Link to this post | posted 03 Feb, 2020 03:41

cdshaffer

This is all happening because of database synchronization issues. Right now pecaan is on 336 and the rest of us have already updated to version 337. You can tell which version in various ways. Since phagesdb.org is always in sync with the web server that publishes the database, you can bookmark this page to see the most current version of the database: http://phamerator.webfactional.com/databases_Hatfull/Actinobacteriophage.version For phamerator.org there is a pulldown menu in the top right with the database version number; for Pecaan the version is noted just above the map on the Pham Maps tab; for starterator the version is noted just after the run date near the top of the text section of the report so any working report can be used. You can also just go to the URL "phages.wustl.edu/<version>/" to see if that version has been posted. For example, to check if version 337 is available go here: http://phages.wustl.edu/337/ All those reports are specific for version 337. Since Pecaan is on an older version than starterator there is a work around. Just change the "starterator" in the url to the database version number. So when pecaan is using the old 336 and it tries to use an out of date link, this one for example http://phages.wustl.edu/starterator/Pham99984Report.pdf it fails with a 404, so knowing Pecaan is using version 336 replace the "starterator" in the URL with the version number like this: http://phages.wustl.edu/336/Pham99984Report.pdf.pdf and now it works. When starterator is behind pecaan there is not much that can be done but wait until I post the newest set; but please feel free to send me an email and I can at least give you an ETA. P.S. the above links may not work correctly once version 338 of the database is released. Edited 03 Feb, 2020 21:28

Link to this post | posted 29 Jan, 2020 22:27
cdshaffer	To adjust the VM desktop image use the virtual box View -> Virtual Screen -> Scale to… menu item. When I am on a high res screen like my macbook pro screen I set "Scale to 200%" and when I am on an external monitor I set "Scale to 100%" but feel free to pick whatever scale works best for you.

Link to this post | posted 21 Jan, 2020 23:15
cdshaffer	The picture you posted looks like you are running an old version of DNA Master. Mine version of that tab looks like the attached. You should double check that you have an up to date version of DNA Master. I just checked and it says: Version 5.23.3 build 2693 from 26 November 2019 which it reports is up to date. 27Kb

Link to this post | posted 21 Jan, 2020 23:06

cdshaffer

With the MLK holiday weekend I was not able to calculate the new reports until this afternoon for the recently posted version of the database. The reports for this release of the database (number 336) has now been posted and pham 106383 is now available. Most missing phams are due to this issue of databases being out of sync. Unfortunately, it takes up to 20 CPU hours to calculate all 14,000 or so Starterator reports. Thus Starterator will typically be the last to update and often up to 1 day later than the other web pages. You can see which version of the database PECAAN is using on the PhamMaps page just above the map; for phamerator.org you can see which version in the pull-down menu near the top left corner; for Starterator the database version is now indicated near the top of the second page just after the date run. If these numbers do not match you can expect a higher risk of missing phams until the new Starterator analysis has been posted.

Link to this post | posted 18 Dec, 2019 00:12

cdshaffer

Sorry about that. Yes, you unfortunately got stuck in the awkward time between when the new version of the database gets uploaded and all the Starterator reports get published to the web. Starterator has the most processing to do on each pham so it will always be the last piece to update. I was able to push the most recent reports to the server late this morning after an overnight run. As the database grows it is taking longer and longer to process all those pham reports and it is now often taking up to 1 full day to get things uploaded. Edited 18 Dec, 2019 00:14

Link to this post | posted 09 Dec, 2019 19:35
cdshaffer	it does not appear that the large overlap is found in the BD2 cluster. Large overlap is found in most other subclusters. Edited 10 Dec, 2019 16:13