SEA-PHAGES | Phage not found in track

Link to this post \| posted 07 Oct, 2015 17:13
karosales	Hi, we're using Starterator in order to annotate our bacteriophage Bipper this semester. We've been choosing Pham for the "choose what you want to starterate" option and when we receive the reports, Bipper is not seen in the track list. In the annotation guide, the example shows that there should be a track in the report with the gene of the phage we are annotating. Is there are reason that Bipper is not coming up on the list or are we doing something wrong?

Link to this post | posted 07 Oct, 2015 17:13

Hi, we're using Starterator in order to annotate our bacteriophage Bipper this semester. We've been choosing Pham for the "choose what you want to starterate" option and when we receive the reports, Bipper is not seen in the track list. In the annotation guide, the example shows that there should be a track in the report with the gene of the phage we are annotating. Is there are reason that Bipper is not coming up on the list or are we doing something wrong?

Link to this post \| posted 08 Oct, 2015 17:28
cdshaffer	I would be happy to look into this. It is pretty unlikely that you are doing something wrong. To start I need to make sure I have the same database to see if I can replicate the problem. If you open up Phamerator and select Edit -> Preferences. You should see something like the picture I attached. Do you see the same Actino_Draft for the Database, or something else? If you do see Actino_Draft, can you check that your Ubuntu machine is able to get to the internet to download the most recent version of the database? To do that just open up a web browser in the ubuntu machine and see if you can get to sites on the internet like seaphages.org. Edited 08 Oct, 2015 17:33 36Kb

Link to this post | posted 08 Oct, 2015 17:28

cdshaffer

I would be happy to look into this. It is pretty unlikely that you are doing something wrong.

To start I need to make sure I have the same database to see if I can replicate the problem. If you open up Phamerator and select Edit -> Preferences. You should see something like the picture I attached. Do you see the same Actino_Draft for the Database, or something else?

If you do see Actino_Draft, can you check that your Ubuntu machine is able to get to the internet to download the most recent version of the database? To do that just open up a web browser in the ubuntu machine and see if you can get to sites on the internet like seaphages.org.

Edited 08 Oct, 2015 17:33

Link to this post \| posted 12 Oct, 2015 15:16
karosales	Yes, the database that I've been using is the Actino_Draft database and Bipper does show up on the Phages list in Phamerator.

Link to this post \| posted 12 Oct, 2015 18:57
cdshaffer	It looks like (based on the new 2016SEAVM) that the default database for Starterator is Mycobactriophage_Draft so even if phamerator has Actino_Draft, Starterator may not be using it. To check your instance, open starterator, go to the top magically appearing menu items and select edit-> preferences. In the dialog box, check that the database name in there also set to Actino_draft. It may still be set to Mycobactriophage_Draft. If so, edit that entry to Actino_Draft and hit OK. Once I had done that with my 2016SEAVM I was able to completely process Bipper (great phage name by the way). Also, since I ran the whole phage to check that everything was working with Bipper, I posted the whole phage starterator analysis report as a PDF here. Feel free to download and use if you want. I will figure out how to update the default database for starterator. I don't have direct access to the code for Starterator but I can post a pull request which should fix the issue once it is accepted. That should fix things for future users. Thanks for being the first and discovering the issue of the old default setting for the starterator database. Edited 12 Oct, 2015 21:45

Link to this post | posted 12 Oct, 2015 18:57

cdshaffer

It looks like (based on the new 2016SEAVM) that the default database for Starterator is Mycobactriophage_Draft so even if phamerator has Actino_Draft, Starterator may not be using it. To check your instance, open starterator, go to the top magically appearing menu items and select edit-> preferences. In the dialog box, check that the database name in there also set to Actino_draft. It may still be set to Mycobactriophage_Draft. If so, edit that entry to Actino_Draft and hit OK. Once I had done that with my 2016SEAVM I was able to completely process Bipper (great phage name by the way).
Also, since I ran the whole phage to check that everything was working with Bipper, I posted the whole phage starterator analysis report as a PDF here. Feel free to download and use if you want.

I will figure out how to update the default database for starterator. I don't have direct access to the code for Starterator but I can post a pull request which should fix the issue once it is accepted. That should fix things for future users. Thanks for being the first and discovering the issue of the old default setting for the starterator database.

Edited 12 Oct, 2015 21:45

Link to this post \| posted 14 Oct, 2015 16:47
karosales	Just checked the Starterator preferences and it turns out it was set to the Mycobacteriophage database. I changed it and tried to Starterate again and it worked! Thank you so much.

Link to this post \| posted 15 Oct, 2015 21:16
cdshaffer	Ok good to know. I will add this issue to the starterator troubleshooting thread.

Link to this post \| posted 17 Mar, 2020 20:40
BillEttinger	In the database (https://phagesdb.org/phams/21962/) The Pham report and starterator report don't equate. The starterator report gives Streptomyces pages from subcluster BE1, while the Pham report are all Microbacterium phages of cluster EG. There is not a listing for Phage Casend (EG) in the Starterator report for Pham 21962. This is also problematic in Pecaan for Phage Casend #52. 29Kb

Link to this post \| posted 18 Mar, 2020 03:34
cdshaffer	This is a database synchronization issue. Phagesdb was on version 347 and the other sites were behind. This can happen anytime a new database is released. It takes a variable amount of time for each site to "catch up". Starterator usually takes about a day as there is a lot of computer work to calculate ~15000 multiple sequence alignments and generate ~15,000 reports, but it is now up to date and should give the correct results. Not sure about PECAAN or phamerator.org. The first thing you should try when you get these discrepancies is check which database each site is on.If they are on different versions This is how you can get the info on which version each site is on: 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

Link to this post | posted 18 Mar, 2020 03:34

cdshaffer

This is a database synchronization issue. Phagesdb was on version 347 and the other sites were behind. This can happen anytime a new database is released. It takes a variable amount of time for each site to "catch up". Starterator usually takes about a day as there is a lot of computer work to calculate ~15000 multiple sequence alignments and generate ~15,000 reports, but it is now up to date and should give the correct results. Not sure about PECAAN or phamerator.org. The first thing you should try when you get these discrepancies is check which database each site is on.If they are on different versions

This is how you can get the info on which version each site is on:
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

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Phage not found in track