SEA-PHAGES | phage that crash starterator

Link to this post \| posted 04 Apr, 2016 19:02
ugolebiewska	Chris, Here is Urszula from QCC. I tried to run Tonenili. Freshly installed Starterator. It crashed on Pham 126 of 261 (which is Pham 9682). I tried both names Tonenili and Tonenili_Draft with the same result. The error message is ValueError: -1 in not in list. Best, Urszula

Link to this post \| posted 04 Apr, 2016 21:49
cdshaffer	Tonenili is a C1 phage, I bet there is a wrap around gene which is causing the crash. I have a version of starterator which tries to recognize this situation and just skip the analysis for that gene. Analysis is running now. I will try running on that version of starterator and see if we can avoid the crash. I will post an update one way or another as soon as I can Edited 05 Apr, 2016 17:01

Link to this post \| posted 04 Apr, 2016 22:15
ugolebiewska	Thank you Chris ! Yes indeed Tonenili has a wrap around gene. Urszula. cdshaffer Tonenili is a C1 phage, I bet there is a wrap around gene which is causing the crash. I have a version of starterator which tries to recognize this situation and just skip the analysis for that gene. Analysis is running now. I will try running on that version of starterator and see if we can avoid the crash. I will post an update one way or another as soon as I can.

Link to this post | posted 04 Apr, 2016 22:15

ugolebiewska

Thank you Chris ! Yes indeed Tonenili has a wrap around gene.
Urszula.

cdshaffer
Tonenili is a C1 phage, I bet there is a wrap around gene which is causing the crash. I have a version of starterator which tries to recognize this situation and just skip the analysis for that gene. Analysis is running now. I will try running on that version of starterator and see if we can avoid the crash. I will post an update one way or another as soon as I can.

Link to this post \| posted 05 Apr, 2016 17:14
cdshaffer	According to the phamerator map, the wrap around gene is pham 9781 I cannot find any proteins in pham 9872 so I am going to guess you have a typo when you put 9782. If that is not the case let me know, I will chase down this discrepancy (could be an issue with a database and be causing the crash). Proceeding with the analysis based on the typo assumption, I can confirm that Tonenili crashes for me on the wrap around gene. I am going to run the version of the program which should skip that gene. These runs take a while I will post again when I have results. Edited 05 Apr, 2016 17:31

Link to this post | posted 05 Apr, 2016 17:14

cdshaffer

According to the phamerator map, the wrap around gene is pham 9781 I cannot find any proteins in pham 9872 so I am going to guess you have a typo when you put 9782. If that is not the case let me know, I will chase down this discrepancy (could be an issue with a database and be causing the crash).

Proceeding with the analysis based on the typo assumption, I can confirm that Tonenili crashes for me on the wrap around gene. I am going to run the version of the program which should skip that gene. These runs take a while I will post again when I have results.

Edited 05 Apr, 2016 17:31

Link to this post \| posted 05 Apr, 2016 18:12
cdshaffer	OK, thanks for that phage, it revealed an error in my code for finding these end spanning genes. I finally got starterator to complete a run with more improvements to the code. You can get the report here. the end spanning gene is not in the report, you will just want to put NA for the starterator notes.

Link to this post \| posted 05 Apr, 2016 18:24
ugolebiewska	Thank you so much Chris !!! Got the report.

Link to this post \| posted 28 Jul, 2016 20:48
lhughes	Chris: I am running the Beta version of Starterator on a phage that I am doing QC on and it is failing. The phage is Sprinklers (C1) and it fails on Pham 192 of 232. Thanks, Lee

Link to this post \| posted 29 Jul, 2016 00:02
washj	Hi Chris, I tried running to generate a report for Jabith using the Beta version of Starterator and it fails at pham 18107 - #42 of 98 It seems that Starterator no longer works as I am no longer able to generate any reports even for a single pham - Itried a couple. Thanks for your help, Jackie Edited 29 Jul, 2016 00:03

Link to this post \| posted 29 Jul, 2016 19:40
cdshaffer	Just back from meetings. I am testing phage Sprinklers now, will test phage jabith after that. If the beta version is failing on everything can you try two things and post the results: 1. Delete all the files in the "Intermediate Files" folder and try the beta version again. How to delete these files is explained in the thread "Read First: Common Starterator Troubleshooting" as item 2 of the first post. I have been having difficulty lately that is solved if I delete all those files. 2. Login to the student account and try the original version of Starterator and post whether things are crashing there or not, this will help isolate problems with the beta version from problems with Starterator in general. If you installed the beta version in the student account just post that you don't have access to the original version anymore. I will also remind any readers that it is a good policy to periodically delete all those files in the "Intermediate Files" folder. Edited 29 Jul, 2016 19:40

Link to this post | posted 29 Jul, 2016 19:40

cdshaffer

Just back from meetings. I am testing phage Sprinklers now, will test phage jabith after that.

If the beta version is failing on everything can you try two things and post the results:

1. Delete all the files in the "Intermediate Files" folder and try the beta version again. How to delete these files is explained in the thread "Read First: Common Starterator Troubleshooting" as item 2 of the first post. I have been having difficulty lately that is solved if I delete all those files.

2. Login to the student account and try the original version of Starterator and post whether things are crashing there or not, this will help isolate problems with the beta version from problems with Starterator in general. If you installed the beta version in the student account just post that you don't have access to the original version anymore.

I will also remind any readers that it is a good policy to periodically delete all those files in the "Intermediate Files" folder.

Edited 29 Jul, 2016 19:40

Link to this post \| posted 30 Jul, 2016 03:38
cdshaffer	OK, I tested Sprinklers on the original version of Starterator and it did not crash. You can download that report from this link. I tested it on Beta version next and it did not crash the first time but when I tried again it did crash. You can download the output from the first run of the beta version with the yellow and green starts from this link. These intermittent problems are very difficult to track down. Can you try the troublshooting solutions given in the first post of the "Read First: Common Starterator Troubleshooting" thread and report back it any of those helped. I wonder if it the problem with either the memory (which can easily change from run to run) or maybe the "Intermediate Files" issue.

Link to this post | posted 30 Jul, 2016 03:38

cdshaffer

OK, I tested Sprinklers on the original version of Starterator and it did not crash. You can download that report from this link.

I tested it on Beta version next and it did not crash the first time but when I tried again it did crash. You can download the output from the first run of the beta version with the yellow and green starts from this link.

These intermittent problems are very difficult to track down. Can you try the troublshooting solutions given in the first post of the "Read First: Common Starterator Troubleshooting" thread and report back it any of those helped. I wonder if it the problem with either the memory (which can easily change from run to run) or maybe the "Intermediate Files" issue.

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phage that crash starterator