SEA-PHAGES | Pham not found in Starterator

Link to this post \| posted 22 May, 2019 16:45
hkotturi	We are working with phage Fulbright and cannot access Starterator reports for the following genes. None of them are orphams. Starterator report 55791 report not found for Gene 43 Fulbright https://phagesdb.org/phams/55791/ Starterator report 55563 report not found for Gene 51 Fulbright https://phagesdb.org/phams/55563/ Starterator report 55854 report not found for Gene 59 Fulbright https://phagesdb.org/phams/55854/ Starterator report 55837 report not found for Gene 65 Fulbright https://phagesdb.org/phams/55837/ Starterator report 55152 report not found for Gene 72 Fulbright https://phagesdb.org/phams/55152/

Link to this post | posted 22 May, 2019 16:45

We are working with phage Fulbright and cannot access Starterator reports for the following genes. None of them are orphams.

Starterator report 55791 report not found for Gene 43 Fulbright
https://phagesdb.org/phams/55791/
Starterator report 55563 report not found for Gene 51 Fulbright
https://phagesdb.org/phams/55563/
Starterator report 55854 report not found for Gene 59 Fulbright
https://phagesdb.org/phams/55854/
Starterator report 55837 report not found for Gene 65 Fulbright
https://phagesdb.org/phams/55837/
Starterator report 55152 report not found for Gene 72 Fulbright
https://phagesdb.org/phams/55152/

Link to this post \| posted 23 May, 2019 10:46
delesall	Also checking annotations for Bunnies and seeing missing starterator reports unavailable in Pecaan and on phagesdb for phams that are not orphams!

Link to this post \| posted 23 May, 2019 10:48
delesall	As an example - Bunnies gene 32 (immunity repressor) pham 56415 (pham number from phagesdb) report is missing

Link to this post \| posted 28 May, 2019 20:12
cdshaffer	I have just returned from vacation and have updated the the starterator pages to the most recent version of the phamerator database which was posted this morning. I checked bunnies gene 32, it is now in pham 39047 and appears to be in sync across pecaan, starterator, phagesdb.org and phamerator.org. Checking phage Fulbright shows some discrepancies across the various platforms but that could be syncronization issues since the last update was posted so recently. I would give it a day and if reports are still missing please repost and I can look into it.

Link to this post | posted 28 May, 2019 20:12

cdshaffer

I have just returned from vacation and have updated the the starterator pages to the most recent version of the phamerator database which was posted this morning. I checked bunnies gene 32, it is now in pham 39047 and appears to be in sync across pecaan, starterator, phagesdb.org and phamerator.org. Checking phage Fulbright shows some discrepancies across the various platforms but that could be syncronization issues since the last update was posted so recently. I would give it a day and if reports are still missing please repost and I can look into it.

Link to this post \| posted 06 Feb, 2020 15:32
coomansr	Annotating Rie18_gp40. Starterator report for pham 109510 not found. Not an orpham and number appears to still be good. Roy

Link to this post \| posted 06 Feb, 2020 17:48
DanRussell	Hi Roy, I think you've caught things between versions of the Phamerator database. If you go to phamerator.org and click on the little dropdown database menu in the top left, it'll show you what version of the database you're currently viewing. As of now, I see Actino_Draft version 338. Meanwhile, Chris has recently made a link where you can check the version of the database Starterator is using. http://phages.wustl.edu/starterator/database.version Earlier today, it showed 337, but I just checked again and now it's showing 338, so hopefully things are back in sync now. –Dan

Link to this post | posted 06 Feb, 2020 17:48

DanRussell

Hi Roy,

I think you've caught things between versions of the Phamerator database. If you go to phamerator.org and click on the little dropdown database menu in the top left, it'll show you what version of the database you're currently viewing. As of now, I see Actino_Draft version 338.

Meanwhile, Chris has recently made a link where you can check the version of the database Starterator is using.
http://phages.wustl.edu/starterator/database.version

Earlier today, it showed 337, but I just checked again and now it's showing 338, so hopefully things are back in sync now.

–Dan

Link to this post \| posted 07 Feb, 2020 18:38
hnance@ccga.edu	Was Starterator just updated? I cannot find any Starterator data for genes that are not orphams. Should I just wait a day to have it updated? All was fine until about 30 minutes ago. I'm not sure how to check my gene list to see if it is up to date as suggested in these other posts. Thanks!

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 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 19 Jul, 2020 18:23
Cland44	Hi Chris- Using the links provided to check versions, I found that starterator and phagesdb are both on version 364, but I'm getting a lot of error 404 messages for starterator. Am I correct in assuming starterator is still updating? Phams 14933, 9485, and 8041 so far, and none of these are orphams. I'm working in cluster AZ, and the pfams seem to mostly be composed of genes from those clusters (exception for 14933). I'll keep track of other pfams that are showing errors in pulling starterator data. –Christie Edited 19 Jul, 2020 18:24

Link to this post | posted 19 Jul, 2020 18:23

Cland44

Hi Chris-
Using the links provided to check versions, I found that starterator and phagesdb are both on version 364, but I'm getting a lot of error 404 messages for starterator. Am I correct in assuming starterator is still updating? Phams 14933, 9485, and 8041 so far, and none of these are orphams. I'm working in cluster AZ, and the pfams seem to mostly be composed of genes from those clusters (exception for 14933). I'll keep track of other pfams that are showing errors in pulling starterator data.

–Christie

Edited 19 Jul, 2020 18:24

Link to this post \| posted 24 Jul, 2020 22:15
cdshaffer	Wow, somehow I missed this message, sorry about that. Yes starterator is still being updated but it often lags behind the other pages. The issue is that right now the Hatfull lab is working on a large refactoring of the database and while these changes are on going all the web pages are much more likely to get out of sync. Exactly which version of the database each web page is on varies. I think phagesdb and phamerator are on version 362 while pecaan and starterator are on version 364. So if you are using pecaan things should work OK but if you are looking for phams based on phagesdb or phamerator.org you need to go to an older version of the starterator reports. To do that just substitute the "starterator" part of the URL with the database number, so to get pham 8041 from database version 362 go to: http://phages.wustl.edu/362/Pham8041Report.pdf And Voilà you have your report. Since most phams stay the same across releases most links from phagesdb should work, but when they don't just substitute in the "362" into the URL. This will work until phagesdb is updated to the current version, at which point all links should work.

Link to this post | posted 24 Jul, 2020 22:15

cdshaffer

Wow, somehow I missed this message, sorry about that.
Yes starterator is still being updated but it often lags behind the other pages. The issue is that right now the Hatfull lab is working on a large refactoring of the database and while these changes are on going all the web pages are much more likely to get out of sync.

Exactly which version of the database each web page is on varies. I think phagesdb and phamerator are on version 362 while pecaan and starterator are on version 364. So if you are using pecaan things should work OK but if you are looking for phams based on phagesdb or phamerator.org you need to go to an older version of the starterator reports. To do that just substitute the "starterator" part of the URL with the database number, so to get pham 8041 from database version 362 go to:

http://phages.wustl.edu/362/Pham8041Report.pdf

And Voilà you have your report. Since most phams stay the same across releases most links from phagesdb should work, but when they don't just substitute in the "362" into the URL. This will work until phagesdb is updated to the current version, at which point all links should work.

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Pham not found in Starterator