Assertion 'params.graph.chainApproxPos[nodeIndex] + realOffset >= seedHits[i].seqPos' failed

[rlorigro]

Hi,

Thanks for this nice contribution to the graph alignment community. I am working on integrating it to one of my pipelines and I get an error on the first run:

Assertion 'params.graph.chainApproxPos[nodeIndex] + realOffset >= seedHits[i].seqPos' failed Read: m64043_200710_174426/70452667/ccs. Seed: 0+,0,0,0
Read m64043_200710_174426/70452667/ccs alignment failed (assertion!)

The input GFA looks like this:

There were multiple reads which failed the assertion, so I reran it which just one read and one thread:

GraphChainer -a test_graphchainer.gaf -g graph_no_empty.gfa -f test.fasta --verbose

which resulted in this output:

GraphChainer Branch master commit 3d2273954299ce413a5eaf1ed6eb6596eb3e485a 2023-03-13 18:15:17 +0200
GraphChainer Branch master commit 3d2273954299ce413a5eaf1ed6eb6596eb3e485a 2023-03-13 18:15:17 +0200
Co-linear chaining on splits=(35,35,10000)
Load graph from graph_no_empty.gfa
Build alignment graph
50 original nodes, 25 in one strand
410 split nodes, 205 in one strand
0 ambiguous split nodes
24706 base pairs (total characters), 12353 in one strand
444 edges, 222 in one strand
12 nodes with in-degree >= 2, 6 in one strand
Build MPC Index
2 connected components
cid = 0 path #0 : 181 181 24
cid = 0 path #0 : 8 4 20
cid = 0 path #0 : 8 4 16
cid = 0 path #0 : 8 4 12
cid = 0 path #0 : 8 4 8
cid = 0 path #0 : 2 2 6
cid = 0 path #0 : 2 2 4
cid = 0 path #0 : 2 2 2
cid = 0 path #0 : 2 2 0
cid = 0 greedy width 9
start shrinkink from width 9
cid = 0 optimal width 9
cid = 0 MPC index done
cid = 1 path #0 : 181 181 24
cid = 1 path #0 : 8 4 20
cid = 1 path #0 : 8 4 16
cid = 1 path #0 : 8 4 12
cid = 1 path #0 : 8 4 8
cid = 1 path #0 : 2 2 6
cid = 1 path #0 : 2 2 4
cid = 1 path #0 : 2 2 2
cid = 1 path #0 : 2 2 0
cid = 1 greedy width 9
start shrinkink from width 9
cid = 1 optimal width 9
cid = 1 MPC index done
MPC building done
total width 18 and max component width 9
Build minimizer seeder from the graph
Minimizer seeds, length 15, window size 20, density 10
Seed cluster size 1
Initial bandwidth 10
write alignments to test_graphchainer.gaf
Align
Read m64043_200710_174426/70452667/ccs seeding took 1ms
src/GraphAligner.h:259: Assertion 'params.graph.chainApproxPos[nodeIndex] + realOffset >= seedHits[i].seqPos' failed. Read: m64043_200710_174426/70452667/ccs. Seed: 0+,0,0,0
Read m64043_200710_174426/70452667/ccs alignment failed (assertion!)
Trying to align long readm64043_200710_174426/70452667/ccsRead m64043_200710_174426/70452667/ccs alignment failed (assertion!)
src/GraphAligner.h:259: Assertion 'params.graph.chainApproxPos[nodeIndex] + realOffset >= seedHits[i].seqPos' failed. Read: m64043_200710_174426/70452667/ccs. Seed: 0+,0,0,0
terminate called after throwing an instance of 'ThreadReadAssertion::AssertionFailure'
Aborted

I have uploaded the GFA and the FASTA here:

https://storage.googleapis.com/rlorigro-public/graphchainer/graph_no_empty.gfa
https://storage.googleapis.com/rlorigro-public/graphchainer/test.fasta

Thanks