SEA-PHAGES | Pham not found in Starterator

Link to this post \| posted 09 Feb, 2021 01:58
ejyoon	Hello, we are annotating Pham 51023 in Figliar, and we can't find a starterator report for this pham. This pham is not an orpham as there are 114 members in this pham. I looked up the pham in phagesDB and it is there, although I do not know how to tell if a pham number has been changed in an update or not. I was hoping to get help with obtaining the starterator report for this pham.

Link to this post \| posted 09 Feb, 2021 19:33
cdshaffer	This was due to a database versioning issue (i.e. starterator was still on version 391 and phagesdb had upated to version 392). The report is now available here. If you want all the details on the how and why this happens, and how to check versions see this thread: this thread If you want to see which version Phamerator.org, pecaan and starterator are on use these instructions: phagesdb see: http://databases.hatfull.org/Actino_Draft/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

Link to this post | posted 09 Feb, 2021 19:33

cdshaffer

This was due to a database versioning issue (i.e. starterator was still on version 391 and phagesdb had upated to version 392). The report is now available here. If you want all the details on the how and why this happens, and how to check versions see this thread: this thread

If you want to see which version Phamerator.org, pecaan and starterator are on use these instructions:
phagesdb see: http://databases.hatfull.org/Actino_Draft/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

Link to this post \| posted 14 Apr, 2021 20:41
SBS_UNL	We are annotating Vine. The pham for gene 74 (start 47825) was 58426 when initially phamerated. It is now pham 57943 (7 members), but a starterator report was not available yesterday, and unavailable today. Version 402 shows for phagesdb and starterator, and phamerator.org. Any insights will be appreciated. Thank you.

Link to this post \| posted 14 Apr, 2021 23:22
debbie	HI! I think this is just an artifact of programs/databases that are not quite caught up to each other. I think if you wait another day, they'll catch up to one another. debbie

Link to this post \| posted 16 Apr, 2021 16:13
cdshaffer	Yes this is a database sync issue. The new database should appear by the end of today. In the mean time the results for vine_74 are still available using the older number you mentioned: http://phages.wustl.edu/starterator/Pham58426Report.pdf The URL has the exact same pattern for all phams, so if get a link that does not work and you see the pham number has changed you can always manually change the URL back to the old number and see if that works. In this case, that 58246 number does work. Sometime later this link will not work. and the newer link will: http://phages.wustl.edu/starterator/Pham57943Report.pdf

Link to this post | posted 16 Apr, 2021 16:13

cdshaffer

Yes this is a database sync issue. The new database should appear by the end of today. In the mean time the results for vine_74 are still available using the older number you mentioned:

http://phages.wustl.edu/starterator/Pham58426Report.pdf

The URL has the exact same pattern for all phams, so if get a link that does not work and you see the pham number has changed you can always manually change the URL back to the old number and see if that works. In this case, that 58246 number does work. Sometime later this link will not work. and the newer link will:

http://phages.wustl.edu/starterator/Pham57943Report.pdf

Link to this post \| posted 17 Apr, 2021 03:39
cdshaffer	OK just an update. The most recent version of the database (403) vine_74 is back to pham 58246. It still appears as pham 57934 on phagesdb so the phagesdb links are out of date and will not work but the first link above will, at some point phagesdb will update and should then report vine_74 is back in pham 58426.

Link to this post \| posted 17 Apr, 2021 16:49
SBS_UNL	cdshaffer OK just an update. The most recent version of the database (403) vine_74 is back to pham 58246. It still appears as pham 57934 on phagesdb so the phagesdb links are out of date and will not work but the first link above will, at some point phagesdb will update and should then report vine_74 is back in pham 58426. Thank you for the followup.

Link to this post \| posted 21 Jun, 2021 14:55
kcornely	Greetings, all, I have a student doing a summer research project and she is annotating the phage Tarkin. There are a number of phams that are not found in Starterator. We've been checking the database regularly, and we can see that the data base number has been changing frequently, so we're assuming that Chris Schaffer is hard at work updating it. Should we wait for the updates or would you like us to send you the pham numbers for the phams that are missing Starterator reports? Thanks very much! Kathleen

Link to this post | posted 21 Jun, 2021 14:55

kcornely

Greetings, all,
I have a student doing a summer research project and she is annotating the phage Tarkin. There are a number of phams that are not found in Starterator. We've been checking the database regularly, and we can see that the data base number has been changing frequently, so we're assuming that Chris Schaffer is hard at work updating it. Should we wait for the updates or would you like us to send you the pham numbers for the phams that are missing Starterator reports?
Thanks very much!
Kathleen

Link to this post \| posted 21 Jun, 2021 17:07
kbutela	Hi Kathleen! Are your students accessing Starterator reports via PECAAN or directly through PhagesDB? If they are using PECAAN, I have a video demonstrating how to solve this issue. kcornely Greetings, all, I have a student doing a summer research project and she is annotating the phage Tarkin. There are a number of phams that are not found in Starterator. We've been checking the database regularly, and we can see that the data base number has been changing frequently, so we're assuming that Chris Schaffer is hard at work updating it. Should we wait for the updates or would you like us to send you the pham numbers for the phams that are missing Starterator reports? Thanks very much! Kathleen

Link to this post | posted 21 Jun, 2021 17:07

kbutela

Hi Kathleen! Are your students accessing Starterator reports via PECAAN or directly through PhagesDB? If they are using PECAAN, I have a video demonstrating how to solve this issue.

kcornely
Greetings, all,
I have a student doing a summer research project and she is annotating the phage Tarkin. There are a number of phams that are not found in Starterator. We've been checking the database regularly, and we can see that the data base number has been changing frequently, so we're assuming that Chris Schaffer is hard at work updating it. Should we wait for the updates or would you like us to send you the pham numbers for the phams that are missing Starterator reports?
Thanks very much!
Kathleen

Link to this post \| posted 21 Jun, 2021 17:21
kcornely	Kristin, we are accessing the reports through phagesdb, but I'd love to see your video! If we can't get the reports on phagesdb, we can go to PECAAN. I'm trying to wait as long as possible to introduce PECAAN because I want the new students to engage as much as possible with all of the other programs used in the annotation. Thanks!

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Pham not found in Starterator