abyss PopBubbles error

Question

[Damian Kao]

I am assembling a potentially highly heterozygous animal. I wanted to modify abyss' PopBubble step to scaffold over complex bubbles. I used the following command in place of the original command during the unitig generation steps:

PopBubbles  --dot -j32 -k49 -p0.85 --scaffold -b 50000 -g k49-3.dot k49-2.fa k49-2.dot > k49-2.path

And it gave me this error:

PopBubbles: PopBubbles.cpp:450: void scaffoldBubble(Graph&, const Bubble&): Assertion `isBubble(g, bubble.begin(), bubble.end())' failed.
Aborted (core dumped)

Any idea how to fix this?

[benv]

Hi Damian,

I'm not the author of PopBubbles, but I have been perusing the code for a few minutes. Unfortunately, it looks like you have uncovered a bug -- some sort of edge case that isn't accounted for by the --scaffold option of PopBubbles.

In order to figure out what is going on, I would need some example .fasta/.dot files to reproduce the problem locally on my machine. Preferably small files so that the debugging process is fast. I will send you my e-mail address in a private message, so that you would be able to send the files to me over e-mail.

I realize that creating such a test data set may not be easy. One thing that may help: I have noticed from the code that verbose level 3 (-vvv) produces some debugging output about the sequences it is currently operating on. Try adding -vvv to you PopBubbles options and see if that gives you some useful information.

[benv]

I don't think there is an option to send private messages to other users on BioStars. My e-mail address is: benv at bcgsc dot ca.

[Damian Kao]

Thanks. I'll try running it again with the -vvv option and send you the results over e-mail.