SEA-PHAGES | phage that crash starterator

Link to this post \| posted 10 Jul, 2015 18:00
edgingtonn1	Yes it made it farther with Snape by deleting the Intermediate files. This time up to Pham 26 out of 100. Here's the error it threw for Snape: Pham 26 of 100 0.26 ? /home/seastudent/Applications/Starterator/starterator/starterator/extras/starterator.config <ConfigParser.RawConfigParser instance at 0xad6500cc> ? /home/seastudent/Applications/Starterator/starterator/starterator/extras/starterator.config <ConfigParser.RawConfigParser instance at 0xabad448c> ? /home/seastudent/Applications/Starterator/starterator/starterator/extras/starterator.config <ConfigParser.RawConfigParser instance at 0xabad484c> exception in starterator Exception in thread Thread-1: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 551, in __bootstrap_inner self.run() File "/home/seastudent/Applications/Starterator/starterator/starterator/uiStarterate.py", line 297, in run self.starterate() File "/home/seastudent/Applications/Starterator/starterator/starterator/uiStarterate.py", line 302, in starterate gui=self, event=self.stop_thread) File "/home/seastudent/Applications/Starterator/starterator/starterator/starterate.py", line 112, in starterate final_file, short_final = phage.final_report() File "/home/seastudent/Applications/Starterator/starterator/starterator/report.py", line 52, in final_report self.make_reports() File "/home/seastudent/Applications/Starterator/starterator/starterator/report.py", line 77, in make_reports pham = gene_report.make_report(whole=True) File "/home/seastudent/Applications/Starterator/starterator/starterator/report.py", line 268, in make_report self.pham.find_most_common_start() File "/home/seastudent/Applications/Starterator/starterator/starterator/phams.py", line 220, in find_most_common_start most_called_start_index = self.total_possible_starts.index(called_starts_count[0][0])+1 ValueError: 45 is not in list Ichabod ran fine after deleting the old temp files!

Link to this post | posted 10 Jul, 2015 18:00

Yes it made it farther with Snape by deleting the Intermediate files. This time up to Pham 26 out of 100.

Here's the error it threw for Snape:

 Pham 26 of 100 0.26
? /home/seastudent/Applications/Starterator/starterator/starterator/extras/starterator.config <ConfigParser.RawConfigParser instance at 0xad6500cc>
? /home/seastudent/Applications/Starterator/starterator/starterator/extras/starterator.config <ConfigParser.RawConfigParser instance at 0xabad448c>
? /home/seastudent/Applications/Starterator/starterator/starterator/extras/starterator.config <ConfigParser.RawConfigParser instance at 0xabad484c>
exception in starterator
Exception in thread Thread-1:
Traceback (most recent call last):
  File "/usr/lib/python2.7/threading.py", line 551, in __bootstrap_inner
    self.run()
  File "/home/seastudent/Applications/Starterator/starterator/starterator/uiStarterate.py", line 297, in run
    self.starterate()
  File "/home/seastudent/Applications/Starterator/starterator/starterator/uiStarterate.py", line 302, in starterate
    gui=self, event=self.stop_thread)
  File "/home/seastudent/Applications/Starterator/starterator/starterator/starterate.py", line 112, in starterate
    final_file, short_final = phage.final_report()
  File "/home/seastudent/Applications/Starterator/starterator/starterator/report.py", line 52, in final_report
    self.make_reports()
  File "/home/seastudent/Applications/Starterator/starterator/starterator/report.py", line 77, in make_reports
    pham = gene_report.make_report(whole=True)
  File "/home/seastudent/Applications/Starterator/starterator/starterator/report.py", line 268, in make_report
    self.pham.find_most_common_start()
  File "/home/seastudent/Applications/Starterator/starterator/starterator/phams.py", line 220, in find_most_common_start
    most_called_start_index = self.total_possible_starts.index(called_starts_count[0][0])+1
ValueError: 45 is not in list

Ichabod ran fine after deleting the old temp files!

Link to this post \| posted 12 Jul, 2015 17:51
cdshaffer	OK I have that same error and stack trace for phage Dori pham 4536. Gene is the last gene and an orpham just ran snape got same crash, pham 26 of 100 ends up being pham 9858 and is also the last gene in the genome and is also an orpham. close inspection shows that this gene spans the ends and is annotated in DNA Master as going from 14 to 51601, however in phamerator the location is listed as just the part at the right end of the genome (i.e. 51601 to 52138 ). The predicted protein sequence is correct in phamerator database just not the right hand coordinate. This eventually leads to the crash. I can see in the code how this is handled for forward strand genes than span the end of the phage, but in these cases the coordinates are correct. Solution to handle this is non-trivial due to need to fix phamerator coordinates Edited 02 Aug, 2015 14:53

Link to this post | posted 12 Jul, 2015 17:51

cdshaffer

OK I have that same error and stack trace for phage Dori pham 4536. Gene is the last gene and an orpham

just ran snape got same crash, pham 26 of 100 ends up being pham 9858 and is also the last gene in the genome and is also an orpham.

close inspection shows that this gene spans the ends and is annotated in DNA Master as going from 14 to 51601, however in phamerator the location is listed as just the part at the right end of the genome (i.e. 51601 to 52138 ). The predicted protein sequence is correct in phamerator database just not the right hand coordinate. This eventually leads to the crash. I can see in the code how this is handled for forward strand genes than span the end of the phage, but in these cases the coordinates are correct. Solution to handle this is non-trivial due to need to fix phamerator coordinates

Edited 02 Aug, 2015 14:53

Link to this post \| posted 16 Jul, 2015 03:37
cdshaffer	phage Amela_Draft from the Actino_Draft database has also been reported to crash starterator.

Link to this post \| posted 19 Jul, 2015 21:05
cdshaffer	more info on phage dori crash the last two genes in dori are problematic, for both of these genes there are no in-frame stop codons upstream of the annotated start codon all the way to the end of the phage. This appears to be causing the crashes. I am slowly working on how best to modify code with minimal risk of breaking something else. Edited 22 Jul, 2015 16:43

Link to this post \| posted 23 Jul, 2015 16:27
anders	TymAbreu_Draft from Actino_Draft causes starterator to stop at gene 24 with "Startstaerator has encountered an error. Please try again". When individual genes are run around 24, it is only 24 that causes the error.

Link to this post \| posted 23 Jul, 2015 20:44
cdshaffer	I tried TymAbreu_draft but that phage was not found, I have the most recent version of the Actino_draft database and in there the phage is no longer "_draft", its just Tymabreu. so I tested it out. Phage ran with no crashes, the likely culprit is confusion between the different "_draft" and current versions of the annotation. I suggest you use phamerator to update the actino_draft database and delete all the files in "Intermediate Files" folder (see the other "troubleshooting starterator" post) then try again. That is likely to work. However in case you need it, I posted the full phage report here. You can download from that link if the above suggestions fail to fix the problem on your system.

Link to this post | posted 23 Jul, 2015 20:44

cdshaffer

I tried TymAbreu_draft but that phage was not found, I have the most recent version of the Actino_draft database and in there the phage is no longer "_draft", its just Tymabreu. so I tested it out. Phage ran with no crashes, the likely culprit is confusion between the different "_draft" and current versions of the annotation. I suggest you use phamerator to update the actino_draft database and delete all the files in "Intermediate Files" folder (see the other "troubleshooting starterator" post) then try again. That is likely to work.

However in case you need it, I posted the full phage report here. You can download from that link if the above suggestions fail to fix the problem on your system.

Link to this post \| posted 22 Oct, 2015 21:23
lhughes	Chris - I am having trouble with Yara_Draft. I've done all the troubleshooting that you list on the "sticky" note in the other topic, but it still crashes at Pham 117 of 135 each time I run it. Lee

Link to this post \| posted 02 Nov, 2015 16:37
cdshaffer	OK I will look into it. Sorry for being late; I am at peak teaching, things should calm considerably. I will try to post updates to this posting as I track down the issue. OK figured out that the 117th pham is pham 14107. This corresponds to gene 1 on the phamerator map. It looks like this is the same (or at least related to) the issue with Dori 94. I have now precisely mapped that gene by running auto-annotation in DNA Master. Turns out the problem gene is a wrap-around gene called by glimmer that goes from base 444 down to base 1, then end of phage down to 68540. Starterator is not able to handle these right now due to the way that they are handled by Phamerator when importing genes like this. Working on a solution…. Ok I did the quick and dirty fix, added code to skip any genes that look problematic. In this case if the length of the gene in the database does not equal the distance between the given start and stop codons then something is awry, so skip the gene. This fix is not yet submitted to the main Starterator branch so your version does not have it, only my local copy. I want to do more testing before I submit. In the mean time I did try my patch on Yara and it went all the way through without crashing. I have posted the final pdf report here. Thanks for the report, another bug squashed! Now if I can just find the time to do all the testing so I can submit all these bug fixes I have found. Edited 03 Nov, 2015 02:10

Link to this post | posted 02 Nov, 2015 16:37

cdshaffer

OK I will look into it. Sorry for being late; I am at peak teaching, things should calm considerably. I will try to post updates to this posting as I track down the issue.

OK figured out that the 117th pham is pham 14107. This corresponds to gene 1 on the phamerator map. It looks like this is the same (or at least related to) the issue with Dori 94.

I have now precisely mapped that gene by running auto-annotation in DNA Master. Turns out the problem gene is a wrap-around gene called by glimmer that goes from base 444 down to base 1, then end of phage down to 68540. Starterator is not able to handle these right now due to the way that they are handled by Phamerator when importing genes like this. Working on a solution….

Ok I did the quick and dirty fix, added code to skip any genes that look problematic. In this case if the length of the gene in the database does not equal the distance between the given start and stop codons then something is awry, so skip the gene. This fix is not yet submitted to the main Starterator branch so your version does not have it, only my local copy. I want to do more testing before I submit. In the mean time I did try my patch on Yara and it went all the way through without crashing. I have posted the final pdf report here. Thanks for the report, another bug squashed! Now if I can just find the time to do all the testing so I can submit all these bug fixes I have found.

Edited 03 Nov, 2015 02:10

Link to this post \| posted 01 Feb, 2016 02:42
lhughes	Chris - having trouble with Picard_Draft. It crashes on Pham 38 or 71. I cleared intermediate files and it still crashed. Lee

Link to this post \| posted 01 Feb, 2016 03:29
lhughes	Lee Hughes Pham 38 or 71. Should be 38 OF 71

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phage that crash starterator