SEA-PHAGES | Read First: Common Starterator Troubleshooting

Link to this post \| posted 25 Jan, 2018 18:07
cdshaffer	It is technically possible to pre-computed whole phage reports for all phage but it is currently unfeasible. Whole phage reports take on average about 5 minutes on a decently powered computer and there are currently over 2300 phage. That works out to about 1 week to calculate all reports. Given that there is a new database every week means I would need 1 computer running full time and totally dedicated to the task. As for Starterator, there is the current "Stable" version that I used to create the report posted above. There is also an "Experimental" version that has a bunch of changes to the output. For comparison here is the output from the "experimental" version: Pollywog_DraftReport_experimental.pdf The experimental version has some improvements that I really like (e.g. sorting of the phage track to the top) that will certainly be in the next "Stable" release, but it also has some parts that still need work (e.g. like the new summary table) and will definitely be changing as soon as the semester calms down and I can get back to coding. Let me know which version you are interested in, and we can go from there.

Link to this post | posted 25 Jan, 2018 18:07

It is technically possible to pre-computed whole phage reports for all phage but it is currently unfeasible. Whole phage reports take on average about 5 minutes on a decently powered computer and there are currently over 2300 phage. That works out to about 1 week to calculate all reports. Given that there is a new database every week means I would need 1 computer running full time and totally dedicated to the task.

As for Starterator, there is the current "Stable" version that I used to create the report posted above. There is also an "Experimental" version that has a bunch of changes to the output. For comparison here is the output from the "experimental" version:

Pollywog_DraftReport_experimental.pdf

The experimental version has some improvements that I really like (e.g. sorting of the phage track to the top) that will certainly be in the next "Stable" release, but it also has some parts that still need work (e.g. like the new summary table) and will definitely be changing as soon as the semester calms down and I can get back to coding.

Let me know which version you are interested in, and we can go from there.

Link to this post \| posted 15 Dec, 2020 16:25
DrCatalase	PEEL K1 cluster phage has several genes (28, 30, and 31) with functions (30 and 31) that have been giving us the… Page/Report not found Error 404 The requested Pham report could not be found. Possible reasons for a missing pham report beyond a simply typo in the URL: 1. Your protein is an orpham (reports are not generated for phams with only one member as there is nothing to compare it to.) Check phagesdb.org for the size of the pham. 2. The phamerator database has been updated and the pham number has changed. You can double check for the correct pham number at phagesdb.org. If neither of the above apply and you believe a report is missing in error it is important that you please post to the seaphages starterator forum. Error for weeks. This is through Pecaan and Phagesdb. Thank you. Sean

Link to this post | posted 15 Dec, 2020 16:25

DrCatalase

PEEL K1 cluster phage has several genes (28, 30, and 31) with functions (30 and 31) that have been giving us the…

Page/Report not found Error 404
The requested Pham report could not be found.

Possible reasons for a missing pham report beyond a simply typo in the URL:

1. Your protein is an orpham (reports are not generated for phams with only one member as there is nothing to compare it to.) Check phagesdb.org for the size of the pham.
2. The phamerator database has been updated and the pham number has changed. You can double check for the correct pham number at phagesdb.org.
If neither of the above apply and you believe a report is missing in error it is important that you please post to the seaphages starterator forum.

Error for weeks. This is through Pecaan and Phagesdb. Thank you.
Sean

Link to this post \| posted 15 Dec, 2020 16:52
cdshaffer	These are typically due to database at phagesdb being out of sync with the current database for the starterator reports but this should not be happening "for weeks". Are you using pecaan or phagesdb for your links? Could you post the pham numbers you are looking for?

Link to this post \| posted 15 Dec, 2020 17:06
DrCatalase	cdshaffer These are typically due to database at phagesdb being out of sync with the current database for the starterator reports but this should not be happening "for weeks". Are you using pecaan or phagesdb for your links? Could you post the pham numbers you are looking for? Used the links from both to doublecheck. Peel 30 pham 45194 Peel 33 pham 45744 Peel 32 pham 45569

Link to this post \| posted 15 Dec, 2020 18:00
cdshaffer	OK this appears to be an out of sync error. The current version of the database is 387. The starterator analysis to create the 14 thousand or so reports is on going so the web pages still report the old version 386. The computations should complete and be posted by the end of the day at which point the links from pecaan and phagesdb should work. In the mean time you can use these links to get to the reports for those three genes in the older 386 database reports here: Peel 30: old pham number 44662 and link http://phages.wustl.edu/386/Pham44662Report.pdf Peel 32:old pham number 44868 and link http://phages.wustl.edu/386/Pham44868Report.pdf Peel 33:old pham number 44899 and link http://phages.wustl.edu/386/Pham44899Report.pdf There is a way to check if the "out of sync" error is likely to be the cause of these types of missing phams by comparing the reported database versions. This link will always show the current version number on the Starterator server. Alternatively, you can look on any starterator report where you will see something like this: "This analysis was run 12/09/20 on database version 386" near the top of the first page of text. In pecaan you can go to the Pham Maps page and look just above the map where you will see something like this: Phamerator Version: 387 . Unfortunately there is no easy way to get the version number of the database at phagesdb but you can always check this link to see which version is on the database server, all the programs download from there. Edited 15 Dec, 2020 20:47

Link to this post | posted 15 Dec, 2020 18:00

cdshaffer

OK this appears to be an out of sync error. The current version of the database is 387. The starterator analysis to create the 14 thousand or so reports is on going so the web pages still report the old version 386. The computations should complete and be posted by the end of the day at which point the links from pecaan and phagesdb should work.

In the mean time you can use these links to get to the reports for those three genes in the older 386 database reports here:

Peel 30: old pham number 44662 and link http://phages.wustl.edu/386/Pham44662Report.pdf
Peel 32:old pham number 44868 and link http://phages.wustl.edu/386/Pham44868Report.pdf
Peel 33:old pham number 44899 and link http://phages.wustl.edu/386/Pham44899Report.pdf

There is a way to check if the "out of sync" error is likely to be the cause of these types of missing phams by comparing the reported database versions. This link will always show the current version number on the Starterator server. Alternatively, you can look on any starterator report where you will see something like this: "This analysis was run 12/09/20 on database version 386" near the top of the first page of text.

In pecaan you can go to the Pham Maps page and look just above the map where you will see something like this: Phamerator Version: 387 . Unfortunately there is no easy way to get the version number of the database at phagesdb but you can always check this link to see which version is on the database server, all the programs download from there.

Edited 15 Dec, 2020 20:47

Link to this post \| posted 15 Dec, 2020 21:05
cdshaffer	ok release of starterator reports for database version 387 are now available and are tagged as the current version. Links from pecaan and phagesdb should now be working (at least until the next database update). Please report if any links fail at this point.

Link to this post \| posted 15 Dec, 2020 21:24
debbie	Chris, You are the best! thanks, debbie

Link to this post \| posted 15 Dec, 2020 22:01
DrCatalase	cdshaffer ok release of starterator reports for database version 387 are now available and are tagged as the current version. Links from pecaan and phagesdb should now be working (at least until the next database update). Please report if any links fail at this point. Thank you, Chris!

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Read First: Common Starterator Troubleshooting