algbio/GraphChainer

output signal 11 and aborted

Closed this issue · 1 comments

I run GraphChainer on a gfa file built using seqwish and a fasta file of reads simulated from one of the genome used to construct the Graph.
I used the command GraphChainer -g graph.gfa -f reads.fa - a alignment.json

I got the following message

GraphChainer Branch master commit c083580a2ca5c9d3772da41d2106d0795de500e6 2022-03-30 09:59:42 +0300
GraphChainer Branch master commit c083580a2ca5c9d3772da41d2106d0795de500e6 2022-03-30 09:59:42 +0300
Co-linear chaining on splits=(35,35,10000)
Load graph from graph.gfa
Build alignment graph
5992064 original nodes, 2996032 in one strand
6131490 split nodes, 3065745 in one strand
0 ambiguous split nodes
21011356 base pairs (total characters), 10505678 in one strand
9087448 edges, 4543724 in one strand
1518594 nodes with in-degree >= 2, 759297 in one strand
Build MPC Index
2 connected components
cid = 0 path #0 : 33195 33195 5950803
cid = 0 path #0 : 33193 16597 5934206
cid = 0 path #0 : 33193 15714 5918492
cid = 0 path #0 : 5125 5125 5913367
cid = 0 path #0 : 5123 2562 5910805
cid = 0 path #0 : 5123 2414 5908391
Signal 11. Read: ��0�4��. Seed: 0+,0,0,0
Aborted

can you help solve this issue?

Please see #3