SEA-PHAGES | Read First: Common Starterator Troubleshooting

Link to this post \| posted 27 Apr, 2016 16:52
cdshaffer	Wow! There were three genes in Kerberos that crashed starterator. These are all issues with protein names that is a known incompatability between Starterator and the phamerator database which needs work. Hopefully this will get addressed this summer. In the mean time I did get a starterator report of all the genes that did not crash (i.e. report is missing the three genes that crash but the rest are there.) I suggest for notes that you just put NA for the starterator comment for those three genes. You can download the complete pdf using this link. Edited 27 Apr, 2016 19:42

Link to this post | posted 27 Apr, 2016 16:52

Wow! There were three genes in Kerberos that crashed starterator. These are all issues with protein names that is a known incompatability between Starterator and the phamerator database which needs work. Hopefully this will get addressed this summer.

In the mean time I did get a starterator report of all the genes that did not crash (i.e. report is missing the three genes that crash but the rest are there.) I suggest for notes that you just put NA for the starterator comment for those three genes.

You can download the complete pdf using this link.

Edited 27 Apr, 2016 19:42

Link to this post \| posted 29 Apr, 2016 00:55
sahas	Thank you so much Chris. Really appreciate it.I had started doubting myself whether I knew how to run starterator!

Link to this post \| posted 14 Jan, 2017 22:49
cmageeney	Hi Chris, I am currently having issues with starterator in the virtual machine. I have been using the website you created to finish the starterator data that students missed for our phage Kevin1. I was looking through the list for pham 21227 and noticed it is not there. Is there any way I can access this in lieu of the virtual machine. Thanks Katie Mageeney Lehigh University

Link to this post \| posted 16 Jan, 2017 17:53
cdshaffer	Katie, you have hit an issue I have been thinking about a lot lately as we change over to a distributed "all web" system. One of the things that phamerator does on occasion is move proteins to different pham numbers as it updates with new phages. It is pretty rare nowadays but it does happen. When this happens its possible for the various web pages to get "out of sync", each displaying info from a different version of the database. This general problem is a pernicious issue across the bioinformatics field so it is a really good teaching moment for your students. Long story short for you: Kevin1 gene 24 was in pham 21227 but it is now in pham 25384. You can see this if you go to phagesdb page for Kevin1 gene 24.

Link to this post | posted 16 Jan, 2017 17:53

cdshaffer

Katie,
you have hit an issue I have been thinking about a lot lately as we change over to a distributed "all web" system. One of the things that phamerator does on occasion is move proteins to different pham numbers as it updates with new phages. It is pretty rare nowadays but it does happen. When this happens its possible for the various web pages to get "out of sync", each displaying info from a different version of the database. This general problem is a pernicious issue across the bioinformatics field so it is a really good teaching moment for your students.

Long story short for you: Kevin1 gene 24 was in pham 21227 but it is now in pham 25384. You can see this if you go to phagesdb page for Kevin1 gene 24.

Link to this post \| posted 17 Jan, 2017 02:04
cmageeney	Thanks Chris! After I wrote this I noticed that I was using an older phamerator file, I had a few more genes move to new phams. Once I updated the phamerator file, I solved my problem. Katie

Link to this post \| posted 28 Nov, 2017 21:27
lblumer	Hi Chris, I have been working with a student annotating phage Kareem and cannot find the Starterator report for pham 18287 on the wustl site nor can I find this pham in a pham search on phagesdb. However, I can find this pham using Starterator directly in my SEA VM. I got the information I needed on this pham, and the suggested start in Starterator, but I do prefer to use your more detailed pham reports. There are approximately 50 members of this pham. If this is a glitch, I just wanted you to know about it.

Link to this post | posted 28 Nov, 2017 21:27

lblumer

Hi Chris,

I have been working with a student annotating phage Kareem and cannot find the Starterator report for pham 18287 on the wustl site nor can I find this pham in a pham search on phagesdb. However, I can find this pham using Starterator directly in my SEA VM.

I got the information I needed on this pham, and the suggested start in Starterator, but I do prefer to use your more detailed pham reports. There are approximately 50 members of this pham.

If this is a glitch, I just wanted you to know about it.

Link to this post \| posted 29 Nov, 2017 16:45
cdshaffer	I think this issue of the phamerator database synchronization is the most pernicious problem out there. I have been trying to think of ways to improve the system but it is tricky given the various distributed programs that use the database. I keep some older versions of the database just for historical records. It looks like the last version of the database with pham 18287 was version 117. You can see the starterator report here (note the 117 in the URL: http://phages.wustl.edu/117/Pham18287Report.pdf That pham is not found in my next stored version (120), with that version the gene Kareem_11 has moved to pham 29797: http://phages.wustl.edu/120/Pham18287Report.pdf When using the SEA VM the only way to update to the most recent version of the phage database is to run phamerator. Once you start phamerator it will check in to see if there is an update, and if so, it will attempt to download and install. Once you get a successful database update then the SEA VM Starterator will match the current online versions.

Link to this post | posted 29 Nov, 2017 16:45

cdshaffer

I think this issue of the phamerator database synchronization is the most pernicious problem out there. I have been trying to think of ways to improve the system but it is tricky given the various distributed programs that use the database.

I keep some older versions of the database just for historical records. It looks like the last version of the database with pham 18287 was version 117. You can see the starterator report here (note the 117 in the URL:

http://phages.wustl.edu/117/Pham18287Report.pdf

That pham is not found in my next stored version (120), with that version the gene Kareem_11 has moved to pham 29797:

http://phages.wustl.edu/120/Pham18287Report.pdf

When using the SEA VM the only way to update to the most recent version of the phage database is to run phamerator. Once you start phamerator it will check in to see if there is an update, and if so, it will attempt to download and install. Once you get a successful database update then the SEA VM Starterator will match the current online versions.

Link to this post \| posted 24 Jan, 2018 19:39
cdherren	Is Starterator in Ubuntu running? I've been trying to run a report for Pollywog_Draft for several days now and it starts, but never makes any progress. I've cleared out the Intermediate Files folder and upped the virtual memory to 2024M.

Link to this post \| posted 24 Jan, 2018 20:52
cdshaffer	Unfortunately the last build of the SEA VM was done before I was able to release the version of Starterator with all the bug fixes. So the SEA VM version will work for many but not all phage. I have run a full phage report for pollywog on the updated version of starterator and you can download it from here: Starterator report on Pollywog. Feel free to download and use but it may not be what would work best for you depending on your didactic goals. If you want include the use of VM's and Starterator in your class then it is probably best to update the VM with the latest version of starterator. It is fairly straight forward, just post a follow-up query on how to update starterator if you are interested. Another alternative is to use the pre-computed starterator reports. This is part of the effort to get away from the VM and get everything available via web browser so it is platform independant. These reports are available as links off of the phagesdb pages for the phams and the individual gene pages. Examples: http://phagesdb.org/phams/431/ (Pham page, click on the blue “Get Starterator Report” button at the top of the page.) http://phagesdb.org/genes/POLLYWOG_DRAFT_9/ (Gene page, click on the link “Pham 431 Report” link in the fourth row of the table.) The good part about these pre-computed reports is that they are updated every time new phage genomes are added to the phamerator database throughout the spring. The whole phage report above may get out of date if more F1 phages are sequenced and added to the database.

Link to this post | posted 24 Jan, 2018 20:52

cdshaffer

Unfortunately the last build of the SEA VM was done before I was able to release the version of Starterator with all the bug fixes. So the SEA VM version will work for many but not all phage.
I have run a full phage report for pollywog on the updated version of starterator and you can download it from here:

Starterator report on Pollywog.

Feel free to download and use but it may not be what would work best for you depending on your didactic goals. If you want include the use of VM's and Starterator in your class then it is probably best to update the VM with the latest version of starterator. It is fairly straight forward, just post a follow-up query on how to update starterator if you are interested. Another alternative is to use the pre-computed starterator reports. This is part of the effort to get away from the VM and get everything available via web browser so it is platform independant. These reports are available as links off of the phagesdb pages for the phams and the individual gene pages. Examples:

http://phagesdb.org/phams/431/
(Pham page, click on the blue “Get Starterator Report” button at the top of the page.)

http://phagesdb.org/genes/POLLYWOG_DRAFT_9/
(Gene page, click on the link “Pham 431 Report” link in the fourth row of the table.)

The good part about these pre-computed reports is that they are updated every time new phage genomes are added to the phamerator database throughout the spring. The whole phage report above may get out of date if more F1 phages are sequenced and added to the database.

Link to this post \| posted 24 Jan, 2018 21:02
cdherren	I still like the inclusive 1 file for an entire phage. Will that ever be an option on the phagesdb site? We group annotate and use 1 copy of a complete Starterator and GeneMark report for working in class. It's also helpful because we hand annotate every ORF on paper and keep a binder for each phage with a cover page, Starterator report, GeneMark reports, tRNA search results, and a single form fill page for each gene we annotate, add, delete, modify, etc. for our permanent records. I generally run Starterator myself and then just provide the pdf for the class, so I would like to update the VM and Starterator on my Mac.

Link to this post | posted 24 Jan, 2018 21:02

cdherren

I still like the inclusive 1 file for an entire phage. Will that ever be an option on the phagesdb site?

We group annotate and use 1 copy of a complete Starterator and GeneMark report for working in class. It's also helpful because we hand annotate every ORF on paper and keep a binder for each phage with a cover page, Starterator report, GeneMark reports, tRNA search results, and a single form fill page for each gene we annotate, add, delete, modify, etc. for our permanent records.

I generally run Starterator myself and then just provide the pdf for the class, so I would like to update the VM and Starterator on my Mac.

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Read First: Common Starterator Troubleshooting