SEA-PHAGES Logo

The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.

Recent Activity

smg366 posted in PhamNexus on SEA-VM

Debbie Jacobs-Sera posted in Assignment of gp28 as holin

nietof posted in Assignment of gp28 as holin

nietof posted in Assignment of gp28 as holin

Debbie Jacobs-Sera posted in Capsid maturation protease and MuF-like fusion protein

All posts created by edgingtonn1

| posted 10 Jul, 2015 18:00
edgingtonn1 avatar
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!
Posted in: Starterator → phage that crash starterator
| posted 07 Jul, 2015 19:00
edgingtonn1 avatar
edgingtonn1
Nicholas Edgington
Nicholas Edgington
Phage Snape crashes Starterator at pham 527 (which has 214 members). It was the second pham of the run (out of 100). I searched/entered both 'Snape' and 'Snape__Draft', and had the same error. Pham 527 corresponds to Snape_gp27. I used the SEA2015 VM, DB= 'Mycobacteriophage_Draft', Phamerator 322.

When I run Starterator on the command line, I see that in line 98 of "phams.py" in :
add_alignment gene= self.genes[record.id]
KeyError: 'Luchador_Draft_27'

When I look at the Phamerator map, Luchador is not a 'draft' genome, and gp27 corresponds to pham 165. Luchador gp28 IS in pham 527. Perhaps Starterator is getting stuck with mismatches between a draft genome sequence and the final (GenBank) genome sequence???
Posted in: Starterator → phage that crash starterator
| posted 07 Jul, 2015 18:52
edgingtonn1 avatar
edgingtonn1
Nicholas Edgington
Phage Ichabod crashes Starterator at pham 3588 (318 members). It was the first pham out of 92 total. I used the SEA2015 VM, DB= 'Mycobacteriophage_Draft', Phamerator 322.

On the command line, I see that Starterator shows in line 98 in "add_alignment":

gene = self.genes[record.id]
KeyError: 'Nerujay_Draft_37'

When I look at the Phamerator map of Nerujay, the genes are labeled like "SEA_NERUJAY_37", and Nerujay is NOT listed as a Draft sequence when I pull it up on the Phamerator Phams list…FWIW.
Posted in: Starterator → phage that crash starterator
| posted 07 Jul, 2015 18:39
edgingtonn1 avatar
edgingtonn1
Nicholas Edgington
Phage Snape crashes Starterator at pham 527 (which has 214 members). It was the second pham of the run (out of 100). I searched/entered both 'Snape' and 'Snape__Draft', and had the same error. Pham 527 corresponds to Snape_gp27. I used the SEA2015 VM, DB= 'Mycobacteriophage_Draft', Phamerator 322.

When I run Starterator on the command line, I see that in line 98 of "phams.py" in :
add_alignment gene= self.genes[record.id]
KeyError: 'Luchador_Draft_27'
Posted in: Starterator → phage that crash starterator
| posted 07 Jul, 2015 18:16
edgingtonn1 avatar
edgingtonn1
Phage Ichabod crashes Starterator at pham 3588 (318 members). It was the first pham out of 92 total. I used the SEA2015 VM, DB= 'Mycobacteriophage_Draft', Phamerator 322.
Posted in: Starterator → phage that crash starterator
| posted 07 Jul, 2015 18:11
edgingtonn1 avatar
edgingtonn1
Phage Snape crashes Starterator at pham 527 (which has 214 members). It was the second pham of the run (out of 100). I searched/entered both 'Snape' and 'Snape__Draft', and had the same error. Pham 527 corresponds to Snape_gp27. I used the SEA2015 VM, DB= 'Mycobacteriophage_Draft', Phamerator 322.
Posted in: Starterator → phage that crash starterator