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Ragtag.py merge RuntimeError: only complete components can be added to the graph error #156
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okay so have moved forward to another error after more trouble shooting. I renamed the column 1 so that the AGPs did not have the same identifiers as the later columns. This makes the NCBI validator throw 0 errors. Yay I am now having similar issue as some other people
I could not identify, from the other issues, a fix for this or why this is occuring. It is the same input assembly that was used for the two different scaffold attempts. Any and all help would be amazing and I am happy to provide more info if you need it :). Ben |
Hi there, Sorry about the delays. I would use standard command line tools to check if both AGP files contain identical sets of AGP components. I understand that it's the same input assembly, but perhaps some of the contigs are left out depending on the scaffolding solution. |
Hi @malonge First of all apologies was on holiday for the past two weeks. I am going to be jumping back into this so will post updates and fixes here if I find them :). Ben |
Good morning @malonge et al 🙂 Apologies for the delay but finally got back to this. So I have successfully trouble shot this as per @malonge suggestion. The problem in the AGP file is in column 6. All contigs from the primary assembly are present and correct, what was actually the problem was different gap sizes input by the ntlink program (default 20) compared to the ragtag (default 100). I am going to run ntlink with the gapsize set to 100, and then see if the merge will successfully work. This should fix the discrepancy and merge should hopefully work :). I will post whether this works and then close the issue after that. Thank you for the help Ben |
Hi, thank you for this easy to use and well documented tool! I am struggling with similar issue and I cannot find a way around it.
HiC scaffolding was done using YaHS and then I did some manual curation in Juicebox. Both the YaHS scaffolding agp and agp converted from Juicebox .assembly file give the same ragtag error. I validated agps (from yahs and juicebox) with your tool and it says there are no errors. When I use the NCBI validator one type of error and several warnings appears: Warnings (one example per type):
Do you have any ideas what could be wrong? I don't know where else to look and what to try. I read in you ragtag paper that you used agp converted from .assembly with some custom script. Did the manual curation involved breaking some contigs? Can you maybe provide the script you mention in the paper? Let me know if I should post some more info. Thank you in advance for any help. |
Hi, -> so ragtag.py merge can not handle the situation whith broken components, i.e. contig breaks!! This seems like a thing that many people will run into. If any scaffolder breaks contigs (e.g. identified a mis-assembly), the resulting AGP can not be used with ragtag merge. Quite disappointing I think. I see a workaround by first breaking both AGPs at these breakpoints, and give new component names to the resulting products. Perhaps another ragtag module can do that? |
Good morning
I have been trouble shooting this for a day to no avail, and as such am posting this question/query about my error message.
Command
I have checked that my agp files are correct using the inbuilt tool, and they are.
Interestingly, when using the NCBI validation tool I get warnings for the contigs that have not (i think) been scaffolded
Would i need to remove these lines with similar information, and only keep in the relevant scaffolded lines (i.e. the top lines as shown below). Or is that a bad idea/100% wrong?
Output from ragtag.py merge
Please also find some additional helpful information from my input files (fasta and the two agps).
Please also find the top 20 contig names from the assembly
Finally, I list my conda environment with installed packages and versions :).
Thank you in advance for any and all help, I am a little stumped with what is going on here.
Ben
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