Throw an error "error: trying to access a snarl tree node of the wrong type" in `haplotypes`
wjwei-handsome opened this issue · 11 comments
1. What were you trying to do?
Haplotype sampling
First step is preprocessing the graph
2. What did you want to happen?
Successfully generate sample.hapl file
3. What actually happened?
Loading GBZ from test.gbz
Generating haplotype information
Guessing that distance index is test.dist
Loading distance index from test.dist
Building minimizer index
Built the minimizer index in 918.913 seconds
Guessing that r-index is test.ri
Loading r-index from test.ri
Determining construction jobs
Using contig name chr12 for chain 0
Partitioned 1 components into 1 jobs in 2.37036 seconds
Running 16 jobs in parallel
error: [job 0]: error: trying to access a snarl tree node of the wrong type
4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:
Place stacktrace here.
5. What data and command can the vg dev team use to make the problem happen?
vg haplotypes -v3 -t16 -H test.hapl test.gbz
6. What does running vg version say?
vg version v1.58.0 "Cartari"
Compiled with g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 on Linux
Linked against libstd++ 20230528
Built by anovak@courtyard.gi.ucsc.edu
Interestingly, I encountered this problem when building dist index before: #3884
So I guess, is there some problem in the distance index when doing haplotypes sampling?
Looking forward to your reply :)
This sounds like an issue with the graph or the distance index. What kind of data do you have, how did you obtain/build the graph, and how did you obtain/build the distance index?
The graph is clip.gfa from the Minigraph-Cactus pipeline, and the distance index was built using the command vg index -t 32 -j test.clip.dist test.clip.gbz.
Additionally, I ran vg haplotype on the graph for each chromosome and found that only chr12 didn't work.
Can you share the graph? I don't think we can figure this out without it.