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phage that crash starterator

| posted 30 Jul, 2016 03:42
cdshaffer avatar
cdshaffer
Ok tried jabith once and it worked all the way through so I posted the results here. That was with the original version.

As with Sprinklers I will try with the beta version see if I can get it to crash there. I will let you know how those go, please if you have time try the solutions suggested above as well and let me know if those stop the crashing.
| posted 30 Jul, 2016 17:54
lhughes avatar
lhughes
Ok - tried Sprinklers again in Beta after clearing Intermediate files. It worked then. Sorry I didn't try that the first time.

Lee
| posted 10 Aug, 2016 18:36
washj avatar
washj
Hi Chris,

Thanks for your help and the file! Starterator is working once again.

Jackie
cdshaffer
Ok tried jabith once and it worked all the way through so I posted the results here. That was with the original version.

As with Sprinklers I will try with the beta version see if I can get it to crash there. I will let you know how those go, please if you have time try the solutions suggested above as well and let me know if those stop the crashing.
| posted 05 Jan, 2017 18:53
coomansr avatar
coomansr
Two of the four phages we had sequenced in December, Aggie and Philonius, would not run on Starterator. Both are Cluster N, and both crashed on pham 21476, which was pham 52 of 70 in Aggie and pham 52 of 72 in Philonius. I am using the new SEA 2017 VM and the database is up to date. Any suggestions?
| posted 06 Jan, 2017 18:41
bjconnor60 avatar
bjconnor60
coomansr
Two of the four phages we had sequenced in December, Aggie and Philonius, would not run on Starterator. Both are Cluster N, and both crashed on pham 21476, which was pham 52 of 70 in Aggie and pham 52 of 72 in Philonius. I am using the new SEA 2017 VM and the database is up to date. Any suggestions?

I have had the same issue with Mattes_Draft on starterator, but crashed just after starting.
| posted 10 Jan, 2017 01:07
cdshaffer avatar
cdshaffer
Sorry everyone but I had some free time to write code over thanksgiving in hopes of getting things into the VM but it was just not soon enough given the timing of the in silico workshop and the need to get the VM out to everyone attending. So if you are using the SEA 2017 and have not updated manually (using git command line), you still have the original version which does crash on quite a few phams.

The current best way to get reports if the SEA 2017 VM crashes on your phage is to use the pham reports I have been posting on the web. I post new reports every time there is a new phamerator database and I use my most recent code so you might find them better than what you are getting from the VM.

You can go here http://phages.wustl.edu/starterator to see a list of all the pham reports for all phams with two or more members, simply scroll down till you find the link for the pham you are interested in and click the link. However given the length of the list, an easier technique is to just type in the address using the pham number since everything else in the address is identical.

For example to get to the report for pham 21476 just type in this address

http://phages.wustl.edu/starterator/Pham21476Report.pdf
| posted 06 Feb, 2017 22:20
edgingtonn1 avatar
edgingtonn1
Flaverint_Draft (A11) crashes at Gene 18 (Pham 8250) with the code below using the Starterator 1.1 from github. (I can however, get the Pham report from the WUSTL website.)

Thanks,
-Nick

CLUSTAL 2.1 Multiple Sequence Alignments

Sequence format is Pearson
Sequence 1: Jabith_Draft_31      204 bp
Sequence 2: Lucivia_Draft_32     204 bp
Sequence 3: Flaverint_Draft_31   204 bp
Sequence 4: Bachome_Draft_31     204 bp
Start of Pairwise alignments
Aligning…

Sequences (1:2) Aligned. Score: 100
Sequences (1:3) Aligned. Score: 100
Sequences (1:4) Aligned. Score: 98.0392
Sequences (2:3) Aligned. Score: 100
Sequences (2:4) Aligned. Score: 98.0392
Sequences (3:4) Aligned. Score: 98.0392
Guide tree file created:   [/home/seafaculty/.starterator/Intermediate Files/Pham8250.dnd]

There are 3 groups
Start of Multiple Alignment

Aligning…
Group 1: Sequences:   2      Score:3876
Group 2: Sequences:   3      Score:3876
Group 3: Sequences:   4      Score:3838
Alignment Score 9738

CLUSTAL-Alignment file created  [/home/seafaculty/.starterator/Intermediate Files/Pham8250.aln]

exception in starterator
Exception in thread Thread-1:
Traceback (most recent call last):
  File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
  File "/home/seafaculty/starterator/starterator/uiStarterate.py", line 296, in run
    self.starterate() #running thread starts here
  File "/home/seafaculty/starterator/starterator/uiStarterate.py", line 301, in starterate
    gui=self, event=self.stop_thread)
  File "/home/seafaculty/starterator/starterator/starterate.py", line 112, in starterate
    final_file, short_final = phage.final_report()
  File "/home/seafaculty/starterator/starterator/report.py", line 59, in final_report
    self.make_reports()
  File "/home/seafaculty/starterator/starterator/report.py", line 84, in make_reports
    pham = gene_report.make_report(whole=True)
  File "/home/seafaculty/starterator/starterator/report.py", line 283, in make_report
    self.pham.find_most_common_start()
  File "/home/seafaculty/starterator/starterator/phams.py", line 233, in find_most_common_start
    most_annot_start_index = self.total_possible_starts.index(annot_starts_count[0][0])+1
IndexError: list index out of range
| posted 08 Feb, 2017 18:09
cdshaffer avatar
cdshaffer
Nick
Pham 8250 does not crash when I use the SEA 2017 VM, so need a bit more background.
Are you using the SEA 2017 VM or something else?
Were you doing a single pham analysis of 8250 or a whole phage report on Flavrint and it crashed on gene 18?
| posted 08 Feb, 2017 18:20
edgingtonn1 avatar
edgingtonn1
Hi Chris,

We were attempting to perform the whole phamerated phage report for Flaverint, and it crashed on gp18. It seems to happen with the 2017VM Starterator, and the Github V1.1 version that I 'git cloned'. In fact, Starterator doesn't seem to like many of the A11's.

Best,
-Nick
| posted 08 Feb, 2017 18:33
cdshaffer avatar
cdshaffer
OK looking into all these reports for phages aggie, philonious and Mattes, it appears these are phams that crash when you do a whole phage report but work when you ask for the individual phams. Very curious bug that will likely need time to solve.
I would recommend that you use the pre-calculated web pages:

for example pham 21476 results are available here:

http://phages.wustl.edu/starterator/Pham21476Report.pdf

Any other pham is available by just changing the pham number in the address above, so to get to pham 123 the URL would be:

http://phages.wustl.edu/starterator/Pham123Report.pdf

The issue I guess is PECAAN which requires a whole phage report, anyone using PECAAN let me know, I will work with you to find the best work around until I can find and fix the bug.
Sorry but since this is not my own code it can be difficult for me to find bugs so I am not sure if it will be easy or difficult to solve this issue.
Edited 08 Feb, 2017 21:22
 
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