SEA-PHAGES | phage that crash starterator

Link to this post \| posted 17 Feb, 2016 23:12
coomansr	Thanks for the file on Roosevelt. I've tried running Mazhar510_Draft 3 times and each time it stops on pham 2 of 87, pham 16401. The other one I ran this week, Royals2015, worked without a hitch! Any help you can provide with Mazhar510 is appreciated. Roy

Link to this post \| posted 19 Feb, 2016 21:27
cdshaffer	Good news, my updated code worked for this one. You can download the complete file here. Wow! over 550 pages, that's some big phams. Sorry it took me so long, too much grading to stop by SEA Phages the last couple days. If anyone is in a hurry feel free to send me an email note that you posted a request and I will get on it, it really doesn't take long to set up the run and then the computer does all the work so don't hesitate to ask! Edited 19 Feb, 2016 21:30

Link to this post | posted 19 Feb, 2016 21:27

cdshaffer

Good news, my updated code worked for this one. You can download the complete file here. Wow! over 550 pages, that's some big phams.

Sorry it took me so long, too much grading to stop by SEA Phages the last couple days.
If anyone is in a hurry feel free to send me an email note that you posted a request and I will get on it, it really doesn't take long to set up the run and then the computer does all the work so don't hesitate to ask!

Edited 19 Feb, 2016 21:30

Link to this post \| posted 19 Feb, 2016 22:05
coomansr	Thanks for the file on Mazhar510, and for the quick turnaround. Roy

Link to this post \| posted 25 Feb, 2016 17:22
nancyljones249	Hi Chris, I've heard such wonderful things about you! We're having a Starterator problem with phage LouisV14. We get to Pham 17 of 64 and it hangs. I've tried several times. We did get our Starterator report for RitaG, first time. LouisV14 is in Phamerator. Any hints what we might try? Thanks, Nancy Jones

Link to this post \| posted 25 Feb, 2016 17:51
ddunbar	Just recently when I try to perform Starterator with my Arthrobacter phage genomes, it crashes by the first or second gene. When I go through Starterator gene by gene only about 25% of them give results. The other genes crash Starterator. I use the Actinobacteriophage draft database for Starterator. Does anyone have any thoughts on how to rectify this issue?

Link to this post \| posted 26 Feb, 2016 16:22
cdshaffer	Nancy, It looks like Starterator was crashing on LouisV14 for an already solved problem, as my local version of starterator with my added code worked just fine and I was able to make a full report. You can download the full report here. David, If I remember correctly the individual gene routine still needs a lot work Starterator crashes on many negative strand genes and if I remember correctly it also does not work well if you give it an orpham. Like you, my early experience in class was very sporadic, some genes worked others did not. Consequently I abandoned that routine in class pretty quickly and worked on getting the whole phage report working since that produced a PDF that could be used for the remainder of the semester. I have not worked on any bugs in the single gene routines at all really, instead, putting what time I could on the bugs that cause the whole phage report to crash. Can you send me the names of one (or two) phage and which pham was being worked on when starterator crashed. I am more interested in which phage cause crashes then doing a whole phamerated phage report as that (I think) is the most important routine to debug but any well documented reports of crashes are always welcome. As long as I get get them to repeatedly crash I can put them on the "to do" list of bugs to investigate and fix. Edited 26 Feb, 2016 18:33

Link to this post | posted 26 Feb, 2016 16:22

cdshaffer

Nancy,
It looks like Starterator was crashing on LouisV14 for an already solved problem, as my local version of starterator with my added code worked just fine and I was able to make a full report. You can download the full report here.

David,
If I remember correctly the individual gene routine still needs a lot work Starterator crashes on many negative strand genes and if I remember correctly it also does not work well if you give it an orpham. Like you, my early experience in class was very sporadic, some genes worked others did not. Consequently I abandoned that routine in class pretty quickly and worked on getting the whole phage report working since that produced a PDF that could be used for the remainder of the semester.

I have not worked on any bugs in the single gene routines at all really, instead, putting what time I could on the bugs that cause the whole phage report to crash. Can you send me the names of one (or two) phage and which pham was being worked on when starterator crashed. I am more interested in which phage cause crashes then doing a whole phamerated phage report as that (I think) is the most important routine to debug but any well documented reports of crashes are always welcome. As long as I get get them to repeatedly crash I can put them on the "to do" list of bugs to investigate and fix.

Edited 26 Feb, 2016 18:33

Link to this post \| posted 26 Feb, 2016 18:26
ddunbar	Chris, thanks for the update! The crashing seems to be happening with the Arthrobacter AK Cluster phages we are working on. I don't want to overwhelm you with "feeding me" Starterator reports since we have seven AK Cluster phages we are working on. The ones that we are currently trying to finish up are the phages Suppi, RcigaStruga, Christian. Canawicakte and Huntingdon.

Link to this post \| posted 26 Feb, 2016 20:31
cdshaffer	Don't worry too much about time. It takes me about 3 minutes to start the run (then the computer works on its own) and about 5 minutes to post the results if they work. If they don't work and still crash starterator then I really do want to document that so we have as complete a list as possible of potential bugs. I got Suppi and RcigaStruga to work just fine with my updated code. I then tried with the original version of Starterator without my code updates and Suppi worked there as well. So now I wonder if this is something specific with your machine. See the sticky first message in the starterator section on common troubleshooting, you should in particular try to delete all the cached Intermediate files (item 2) as that can cause problems if you try to run starterator on phage and the phage get updates in the database. If your phage are still crashing I wonder if you have a corrupted database. You might want to try opening phamerator and doing a force database update. Also try a couple of machines see if you get crashes on only one or all of them. If all those don't help let me know, I can post more reports. easy enough to do over the weekend.

Link to this post | posted 26 Feb, 2016 20:31

cdshaffer

Don't worry too much about time. It takes me about 3 minutes to start the run (then the computer works on its own) and about 5 minutes to post the results if they work. If they don't work and still crash starterator then I really do want to document that so we have as complete a list as possible of potential bugs.

I got Suppi and RcigaStruga to work just fine with my updated code. I then tried with the original version of Starterator without my code updates and Suppi worked there as well. So now I wonder if this is something specific with your machine.

See the sticky first message in the starterator section on common troubleshooting, you should in particular try to delete all the cached Intermediate files (item 2) as that can cause problems if you try to run starterator on phage and the phage get updates in the database.
If your phage are still crashing I wonder if you have a corrupted database. You might want to try opening phamerator and doing a force database update. Also try a couple of machines see if you get crashes on only one or all of them. If all those don't help let me know, I can post more reports. easy enough to do over the weekend.

Link to this post \| posted 26 Feb, 2016 21:33
ddunbar	Chris, many thanks!!

Link to this post \| posted 26 Feb, 2016 23:43
ddunbar	Chris, I deleted the intermediate files as per your instructions. Starterator still crashed on me when I tried it on any of the AK cluster phages we are working on (Suppi, RcigaStruga, Christian, Huntingdon and Canowicakte. I was successful in getting the Starterator file for Suppi but was asked to create a Wash U account username and password to access the Starterator file for RcigaStruga. It looks like I would have to pay a fee to generate a username and password. Would it be possible for you to send me the files as email attachments (dunbardavid75@gmail.com). On a similar note, I logged on and off still could not get Starterator to work. I'm guessing it's my virtual machine that is given me the issues. Strange, however, that up until a week ago Starterator worked fine for me and now is doesn't even trying your "fix". Thanks, David

Link to this post | posted 26 Feb, 2016 23:43

ddunbar

Chris, I deleted the intermediate files as per your instructions. Starterator still crashed on me when I tried it on any of the AK cluster phages we are working on (Suppi, RcigaStruga, Christian, Huntingdon and Canowicakte. I was successful in getting the Starterator file for Suppi but was asked to create a Wash U account username and password to access the Starterator file for RcigaStruga. It looks like I would have to pay a fee to generate a username and password. Would it be possible for you to send me the files as email attachments (dunbardavid75@gmail.com).

On a similar note, I logged on and off still could not get Starterator to work. I'm guessing it's my virtual machine that is given me the issues. Strange, however, that up until a week ago Starterator worked fine for me and now is doesn't even trying your "fix".

Thanks,
David

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phage that crash starterator