SEA-PHAGES | Read First: Common Starterator Troubleshooting

Link to this post \| posted 10 Feb, 2016 22:18
cdshaffer	I did a bunch of debugging last summer/early fall. I was able to fix some of the "off by 1" errors and figure out why some of the phage genes were failing. Starterator is a pretty large and sophisticated and I still don't have a good handle on how it does everything, that would take many hours of reading and thinking about the code which I just don't have time to do right now. I have been reticent to push my fixes out to everyone. First, because I don't really understand everything, I was worried that my changes would create problems for some small percentage of phage even as it fixed problems for others. Also, not all my solutions are high quality. For example, starterator was crashing on negative strand genes that wrap around the end of the sequence. I could not figure out a way to fix this bug without substantially rewriting a huge chunk. So instead I just added a tiny bit of code so starterator just skips over those gene. Not ideal, but better to have a report with all but one gene instead of no report at all. It's one thing for me to change starterator for myself, it's something else entirely for me to set that as the policy for every copy of starterator out there. I will say I am feeling more confident that my modifications do not causes more harm that good now that I have run about half a dozen phage through with no new errors that did not show up with the standard code base. Maybe we should have a few beta testers each try several phage with my code before we push them out to everyone. All my changes are freely available if anyone wants to download them and try their phage. You can get my version of the code from my github repository (github.com cdshaffer/starterator). Anyone comfortable with using the git command line to pull from a remote directory can easily download and test the code. My most recent branch is called filterSpanningGenes.

Link to this post | posted 10 Feb, 2016 22:18

I did a bunch of debugging last summer/early fall. I was able to fix some of the "off by 1" errors and figure out why some of the phage genes were failing. Starterator is a pretty large and sophisticated and I still don't have a good handle on how it does everything, that would take many hours of reading and thinking about the code which I just don't have time to do right now.

I have been reticent to push my fixes out to everyone. First, because I don't really understand everything, I was worried that my changes would create problems for some small percentage of phage even as it fixed problems for others. Also, not all my solutions are high quality. For example, starterator was crashing on negative strand genes that wrap around the end of the sequence. I could not figure out a way to fix this bug without substantially rewriting a huge chunk. So instead I just added a tiny bit of code so starterator just skips over those gene. Not ideal, but better to have a report with all but one gene instead of no report at all. It's one thing for me to change starterator for myself, it's something else entirely for me to set that as the policy for every copy of starterator out there.

I will say I am feeling more confident that my modifications do not causes more harm that good now that I have run about half a dozen phage through with no new errors that did not show up with the standard code base. Maybe we should have a few beta testers each try several phage with my code before we push them out to everyone.

All my changes are freely available if anyone wants to download them and try their phage. You can get my version of the code from my github repository (github.com cdshaffer/starterator). Anyone comfortable with using the git command line to pull from a remote directory can easily download and test the code. My most recent branch is called filterSpanningGenes.

Link to this post \| posted 11 Feb, 2016 14:17
DanRussell	cdshaffer …All my changes are freely available if anyone wants to download them and try their phage. You can get my version of the code from my github repository (github.com cdshaffer/starterator). Anyone comfortable with using the git command line to pull from a remote directory can easily download and test the code. My most recent branch is called filterSpanningGenes. Thanks again, Chris, for all this work. I think we should definitely formulate a plan to get an improved version of Starterator out to everyone. Perhaps it's something that could be part of the Faculty Retreat/Workshop this year and follow it up with some testing. It'd be great to even fix just some of the basic errors. –Dan

Link to this post | posted 11 Feb, 2016 14:17

DanRussell

cdshaffer
…All my changes are freely available if anyone wants to download them and try their phage. You can get my version of the code from my github repository (github.com cdshaffer/starterator). Anyone comfortable with using the git command line to pull from a remote directory can easily download and test the code. My most recent branch is called filterSpanningGenes.

Thanks again, Chris, for all this work. I think we should definitely formulate a plan to get an improved version of Starterator out to everyone. Perhaps it's something that could be part of the Faculty Retreat/Workshop this year and follow it up with some testing. It'd be great to even fix just some of the basic errors.

–Dan

Link to this post \| posted 11 Feb, 2016 23:00
GregFrederick@letu.edu	Chris. Thanks for all the work on bug fixes in Starterator. (I'd send you a PM if I knew how in this system.) Could I persuade you to run Gideon_Draft on your version of Starterator for us and send me a link to the report? I promise to buy you a cup of coffee the next time we are at an HHMI function together!

Link to this post \| posted 12 Feb, 2016 17:42
cdshaffer	Not a problem really, takes about 3 minutes to start things rolling and then everything runs in the background. Then takes another 3 or 4 minutes to post to box and copy the shared link. Gideon did run just fine so it is likely a known bug. Here is the report.

Link to this post \| posted 12 Feb, 2016 18:01
GregFrederick@letu.edu	cdshaffer Not a problem really, takes about 3 minutes to start things rolling and then everything runs in the background. Then takes another 3 or 4 minutes to post to box and copy the shared link. Gideon did run just fine so it is likely a known bug. Excellent. You are awesome! Just for information sake. It was crashing at feature 13 when we tried to run it. I don't know if that info will help with diagnosis or not… But now you have it! Thanks so much! Greg

Link to this post | posted 12 Feb, 2016 18:01

GregFrederick@letu.edu

cdshaffer
Not a problem really, takes about 3 minutes to start things rolling and then everything runs in the background. Then takes another 3 or 4 minutes to post to box and copy the shared link.

Gideon did run just fine so it is likely a known bug.

Excellent. You are awesome! Just for information sake. It was crashing at feature 13 when we tried to run it. I don't know if that info will help with diagnosis or not… But now you have it!

Thanks so much! Greg smile

Link to this post \| posted 16 Apr, 2016 13:24
ddunbar	Dear Chris, last night I did the Starterator report on phage Pitadog and it went fine. For phage Nightmare Starerator gets "hung up" on gp3 with an error message. If and when you have time, could you please look into whether you are having a similar issue with the Nightmare Starterator report? Thanks, David

Link to this post \| posted 16 Apr, 2016 15:42
ddunbar	Chris, actually I meant that the issue in Starterator with is with phage Jordan, not phage Nightmare. It's phage Jordan where we receive the error message starting at gene gp3. quote="david dunbar"]Dear Chris, last night I did the Starterator report on phage Pitadog and it went fine. For phage Nightmare Starerator gets "hung up" on gp3 with an error message. If and when you have time, could you please look into whether you are having a similar issue with the Nightmare Starterator report? Thanks, David

Link to this post | posted 16 Apr, 2016 15:42

ddunbar

Chris, actually I meant that the issue in Starterator with is with phage Jordan, not phage Nightmare. It's phage Jordan where we receive the error message starting at gene gp3.

quote="david dunbar"]Dear Chris, last night I did the Starterator report on phage Pitadog and it went fine. For phage Nightmare Starerator gets "hung up" on gp3 with an error message. If and when you have time, could you please look into whether you are having a similar issue with the Nightmare Starterator report?

Thanks,
David

Link to this post \| posted 19 Apr, 2016 14:05
cdshaffer	Good news, my run worked. Link to full report. Edited 19 Apr, 2016 15:01

Link to this post \| posted 19 Apr, 2016 16:57
ddunbar	Thanks Chris for all your help!!!! On another desktop computer after reinstalling the virtual machine, etc I finally got Starterator to work for Jordan.

Link to this post \| posted 26 Apr, 2016 20:39
sahas	Hello Sorry to bother you again. I have been trying to run Starterator for Kerberos but it seems to stall after Pham 61. Can you please check? Many thanks Sangha

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Read First: Common Starterator Troubleshooting