I wanted to test if my PBJelly installation runs well, so I run it with the provided jellyExample.
Since I got the following Message during execution of the extranction stage, I want to make shure if everything went well anyway:
2017-01-23 09:20:35,463 [WARNING] It is unknown if networkx version 1.11 will work.
2017-01-23 09:20:35,464 [WARNING] If you get an error here, please report it!!!
I'm also wonderig if such messages during support stage should appear:
2017-01-23 09:18:38,414 [WARNING] Read ['m130725_000747_00121_c100518582550000001823079209281362_s1_p0/31986/662_3287'] self-extends Node ref0000003e5 Possible Evidence of Tandem Repeat on Singleton
Are there some output files I can compare my output to or how else can I tell if the PBJelly test got the expected results?
I'm a little bit confused since PBJelly produces a result althoug there are the mentioned warnings.
Since I'm running the program on a server, I cannot change the Networkx version myself and it can take some time until it was changed. (Just to tell you why I didn't change the Networkx version already)
Any help would be appreciated (:
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Hi, you can use summarizeAssembly.py on your output assembly. There should only be a single contig output the test was successful. The networkx 1.1 is untested, so I can't say it it will work, hence the error.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I wanted to test if my PBJelly installation runs well, so I run it with the provided jellyExample.
Since I got the following Message during execution of the extranction stage, I want to make shure if everything went well anyway:
I'm also wonderig if such messages during support stage should appear:
Are there some output files I can compare my output to or how else can I tell if the PBJelly test got the expected results?
I'm a little bit confused since PBJelly produces a result althoug there are the mentioned warnings.
Since I'm running the program on a server, I cannot change the Networkx version myself and it can take some time until it was changed. (Just to tell you why I didn't change the Networkx version already)
Any help would be appreciated (:
Hi, you can use summarizeAssembly.py on your output assembly. There should only be a single contig output the test was successful. The networkx 1.1 is untested, so I can't say it it will work, hence the error.
Thank you for the answer!
There is only one sequence in my result, so it worked (:
Here is my output of summarizeAssembly.py in case that someone else is interested in it: