Comments (8)
Can you also share the commands you used to make the graph, map reads, and make the pack file? Often these errors result from some mismatch between the graphs used at different stages in the analysis.
from vg.
from vg.
Presumably this is new sequencing data, despite using the same graphs, correct?
In any case, nothing jumps out to me as incorrect in the pipeline, although you don't seem to be actually using all of the indexes/graphs that you create. Are you able to share the data?
from vg.
from vg.
Ideally, the d2 GBZ file, the full GBZ, and the sequences you're mapping.
Before that though, can you check what happens if you use spp-pg.xg
instead of spp-pg.d2.xg
in vg call
?
from vg.
from vg.
from vg.
Glad it worked out!
from vg.
Related Issues (20)
- Feature request: Accept jellyfish kmer counts for vg haplotypes HOT 2
- Using vg to analyze transcriptomic data from a mixed background HOT 4
- `vg giraffe` for long reads HOT 1
- Missing '--alt-prefix' option in recent versions of vg deconstruct.
- Problem with vg autoindex with phased VCF HOT 2
- No sample & read group field in BAM output with vg map HOT 5
- I cant get .vg file using vg construct HOT 2
- `vg autoindex` fails on GFA file containing 20k SARS-CoV-2 sequences. HOT 1
- vg giraffe mapping HiFi HOT 1
- error vg autoindex: Input is not sufficient to create indexes HOT 2
- Oddly high mapping quality when aligning reads with Ns HOT 6
- Release vg v1.56.0
- I have a question about gam file. HOT 2
- vg surject: incorrect behavior near polymorphic {repetitive} insertions HOT 4
- Can vg construct a trans-chromosomal graph ? HOT 5
- vg construct will let you create a graph without reference paths, with different path names than Cactus
- VG convert to gfa and back will drop path data. HOT 7
- ERROR: Signal 6 occurred. VG has crashed. Terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc HOT 1
- VG has crashed
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from vg.