SEA-PHAGES | phage that crash starterator

Link to this post \| posted 05 Jul, 2015 17:34
cdshaffer	This is a thread to collect the names of phage that crash Starterator. If you run across a phage that crashes phamerator, start by looking at the troubleshooting thread for things to try to get your things to work. If those tricks fail, please add your phage to the list below. For debugging purposes it would be very helpful to know the database and the specific pham that starterator was working on at the time of the error. The database is very likely "Mycobacteriophage_draft" unless it was specifically changed by the user. The exact value can be found by going to the starterator Edit -> Preferences menu and looking in the "Database Name" field. The pham can be seen in the Starterator status window which will be just behind the window with the crash message. See attachment for an example picture. Edited 12 Jul, 2015 20:12 21Kb

Link to this post | posted 05 Jul, 2015 17:34

This is a thread to collect the names of phage that crash Starterator. If you run across a phage that crashes phamerator, start by looking at the troubleshooting thread for things to try to get your things to work. If those tricks fail, please add your phage to the list below. For debugging purposes it would be very helpful to know the database and the specific pham that starterator was working on at the time of the error.

The database is very likely "Mycobacteriophage_draft" unless it was specifically changed by the user. The exact value can be found by going to the starterator Edit -> Preferences menu and looking in the "Database Name" field.

The pham can be seen in the Starterator status window which will be just behind the window with the crash message. See attachment for an example picture.

Edited 12 Jul, 2015 20:12

Link to this post \| posted 05 Jul, 2015 17:42
cdshaffer	Phage Mana crashes starterator. The exact pham where this occurs is unknown but I found the issue was a name confusion with phage Manad (probably because Mana in contained entirely within Mannad). I found that by entering the whole name as found in phamerator "Mana_draft" that the whole phage report was able to complete successfully.

Link to this post \| posted 05 Jul, 2015 17:45
cdshaffer	Phage Redi crashes starterator at pham 3635, mycobacteriophage_draft database

Link to this post \| posted 05 Jul, 2015 17:45
cdshaffer	Phage Dori crashes starterator at pham 4563 mycobacteriophage_draft database see more info below on this crash Edited 19 Jul, 2015 17:14

Link to this post \| posted 07 Jul, 2015 18:11
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.

Link to this post \| posted 07 Jul, 2015 18:16
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.

Link to this post \| posted 07 Jul, 2015 18:39
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'`

Link to this post | posted 07 Jul, 2015 18:39

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'

Link to this post \| posted 07 Jul, 2015 18:52
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.

Link to this post | posted 07 Jul, 2015 18:52

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.

Link to this post \| posted 07 Jul, 2015 19:00
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???

Link to this post | posted 07 Jul, 2015 19:00

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???

Link to this post \| posted 08 Jul, 2015 21:53
cdshaffer	Yes I see that the current phamerator database now has nerujay and luchador out of draft stage. When I try on my local SEA 2015 image with same version of phamerator and database those phage work for me through the first 10 or so phams, so it looks like these issues might be local to your machine. From what I now understand about starterator I would suggest you try deleting all the old cache files in "/home/seastudent/.sterterator/Intermediate Files/". If that solves the issue we should probably add that to the instructions to try that first before posting about crashing phages. Edited 19 Jul, 2015 17:15

Link to this post | posted 08 Jul, 2015 21:53

cdshaffer

Yes I see that the current phamerator database now has nerujay and luchador out of draft stage. When I try on my local SEA 2015 image with same version of phamerator and database those phage work for me through the first 10 or so phams, so it looks like these issues might be local to your machine. From what I now understand about starterator I would suggest you try deleting all the old cache files in "/home/seastudent/.sterterator/Intermediate Files/". If that solves the issue we should probably add that to the instructions to try that first before posting about crashing phages.

Edited 19 Jul, 2015 17:15

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phage that crash starterator