SEA-PHAGES | phage that crash starterator

Link to this post \| posted 08 May, 2017 20:00
kcornely	Thank you so much, Chris! Sorry to tear you away from your grading. We are used to the standard format, so what you have provided is fine. Thanks again and good luck with the end of the semester!

Link to this post \| posted 08 May, 2017 21:52
kcornely	Thank you so much, Chris! Sorry to take you away from your grading. We are used to using the standard format,so what you have provided is fine. Thanks again and good luck with finals!

Link to this post \| posted 27 Jan, 2019 22:50
kcornely	Hello all! This looks like an old thread, but I'm having trouble with Starterator so this seems to be a good location to post. I'm trying to run Starterator on Skippy, and I selected "Whole Phameratated Phage" and was told that Skippy was not in the database. I know that there is a way to update the database, but I can't remember how, so I chose "Unphamerated Phage" instead and uploaded the FastA file. Starterator appeared to start, but then crashed and I was told to "Please try again" which I did, but it crashed again. Thanks in advance for any help you can provide!

Link to this post | posted 27 Jan, 2019 22:50

kcornely

Hello all! This looks like an old thread, but I'm having trouble with Starterator so this seems to be a good location to post. I'm trying to run Starterator on Skippy, and I selected "Whole Phameratated Phage" and was told that Skippy was not in the database. I know that there is a way to update the database, but I can't remember how, so I chose "Unphamerated Phage" instead and uploaded the FastA file. Starterator appeared to start, but then crashed and I was told to "Please try again" which I did, but it crashed again. Thanks in advance for any help you can provide!

Link to this post \| posted 28 Jan, 2019 16:11
cdshaffer	To update the database use Phamerator, just start up Phamerator, then wait for the download and install. Once Phamerator is done updating Starterator should find phage Skippy. As for "Unphamerator phage", Starterator works much better if you add the Profile in addition to the fasta file. This file gives the locations of all the genes so Starterator does not need to try and figure it out. This file is generated by opening the DNA Master file for the phage and using the default settings of the Genome -> Profile… menu to create and save a .csv file. Transfer that file to your machine running Starterator and use it for the Profile. Finally, all starterator reports are now available online if you don't want to hassle with the whole phage report. They can be accessed from the phagesdb web page for the gene. Here is an example for skippy gene 1: https://phagesdb.org/genes/SKIPPY_DRAFT_1/ On that page is a link to the most recent Starterator Report (currently pham 6729).

Link to this post | posted 28 Jan, 2019 16:11

cdshaffer

To update the database use Phamerator, just start up Phamerator, then wait for the download and install. Once Phamerator is done updating Starterator should find phage Skippy.

As for "Unphamerator phage", Starterator works much better if you add the Profile in addition to the fasta file. This file gives the locations of all the genes so Starterator does not need to try and figure it out. This file is generated by opening the DNA Master file for the phage and using the default settings of the Genome -> Profile… menu to create and save a .csv file. Transfer that file to your machine running Starterator and use it for the Profile.

Finally, all starterator reports are now available online if you don't want to hassle with the whole phage report. They can be accessed from the phagesdb web page for the gene. Here is an example for skippy gene 1:

https://phagesdb.org/genes/SKIPPY_DRAFT_1/

On that page is a link to the most recent Starterator Report (currently pham 6729).

Link to this post \| posted 28 Jan, 2019 22:15
kcornely	Thanks for your suggestion about the profile, Chris! And I did see that all of the starterator genes were on line. But I wanted a full report so that I could upload it to PECAAN. And once I looked up how to upload the database, Starterator worked fine. Thanks again!

Link to this post \| posted 29 Jan, 2019 04:53
lhughes	Kathleen Cornely Thanks for your suggestion about the profile, Chris! And I did see that all of the starterator genes were on line. But I wanted a full report so that I could upload it to PECAAN. And once I looked up how to upload the database, Starterator worked fine. Thanks again! You don't have to upload the Starterator report in PECAAN. Once you upload the FASTA and the GeneMark file, the data for the Starterator reports will link automatically for each gene. Lee

Link to this post | posted 29 Jan, 2019 04:53

lhughes

Kathleen Cornely
Thanks for your suggestion about the profile, Chris! And I did see that all of the starterator genes were on line. But I wanted a full report so that I could upload it to PECAAN.

And once I looked up how to upload the database, Starterator worked fine. Thanks again!

You don't have to upload the Starterator report in PECAAN. Once you upload the FASTA and the GeneMark file, the data for the Starterator reports will link automatically for each gene.

Lee

Link to this post \| posted 04 Feb, 2019 13:13
kcornely	Greetings all! This looks like an old thread, but it seemed appropriate to post here as our phage also crashes when we run Starterator. Zolita crashes routinely at gene 74. I've attached a screenshot to illustrate what happens. Thanks in advance for any help you can provide! 632Kb

Link to this post \| posted 04 Feb, 2019 19:08
cdshaffer	It appears from your picture that you are still running an older version of Starterator. The newer version does not crash. Updating starterator is non-trivial which is one of the reasons we went with online reports. I have posted a whole phage report for phage Zolita which you can download. If you want to try to update, I can help you with that just post a followup or email me directly (address is my last name @ wustl.edu).

Link to this post | posted 04 Feb, 2019 19:08

cdshaffer

It appears from your picture that you are still running an older version of Starterator. The newer version does not crash. Updating starterator is non-trivial which is one of the reasons we went with online reports.
I have posted a whole phage report for phage Zolita which you can download.
If you want to try to update, I can help you with that just post a followup or email me directly (address is my last name @ wustl.edu).

Link to this post \| posted 18 Mar, 2019 19:40
ascherer	Phage Suerte crashes starterator at pham 49881 (pham 56 of 76). The database is actino_draft.

Link to this post \| posted 20 Mar, 2019 16:23
cdshaffer	Hmmm, that pham no longer exists, probably was in the old database but not the newest one, if you are using the virtual machine it is important to run phamerator first to check for and install any database updates before running starterator. I have used the most recent "stable" version of starterator which has a few udpates that you have not seen if you are used to the whole phage report from the version in the virtual machine, so just be aware that the output will be a bit different. I have posted the results here: https://wustl.box.com/s/irzr8fel3z6e1tmr9qirymj3fl91j0ng You should also know that most users no longer bother with the whole phage reports but instead go to the pre-computed online versions of the per pham starterator reports. You can see in this article how to get access to those online reports. I always try to keep these reports up to date with new versions of the database.

Link to this post | posted 20 Mar, 2019 16:23

cdshaffer

Hmmm, that pham no longer exists, probably was in the old database but not the newest one, if you are using the virtual machine it is important to run phamerator first to check for and install any database updates before running starterator.

I have used the most recent "stable" version of starterator which has a few udpates that you have not seen if you are used to the whole phage report from the version in the virtual machine, so just be aware that the output will be a bit different. I have posted the results here:

https://wustl.box.com/s/irzr8fel3z6e1tmr9qirymj3fl91j0ng

You should also know that most users no longer bother with the whole phage reports but instead go to the pre-computed online versions of the per pham starterator reports. You can see in this article how to get access to those online reports. I always try to keep these reports up to date with new versions of the database.

Recent Activity

phage that crash starterator