issue with PoreC based scaffolding #110
Description
Hi,
I have generated PoreC reads based alignment BAM file, followed by picard markduplicate, then trying to generate more contiguous scaffolded genome for my initial assembly fasta but getting following error. I have used nanopore data, ultralong and porec reads to generate initial assembly with 88 contigs and genome size of 750 MB around.
yahs assembly.fasta PoreC_aligned_dedup.bam --file-type BAM
[I::telo_finder] found telo motif AAACCCT in sequence seq000080 5'-end up to position 4894
[I::telo_finder] found telo motif AAACCCT in sequence seq000150 3'-end from position 6879235
[I::telo_finder] found telo motif AAACCCT in sequence seq000170 5'-end up to position 997
[I::telo_finder] found telo motif AAACCCT in sequence seq000200 5'-end up to position 4468
[I::telo_finder] found telo motif AAACCCT in sequence seq000210 3'-end from position 13756492
[I::telo_finder] found telo motif AAACCCT in sequence seq000230 3'-end from position 16794749
[I::telo_finder] found telo motif AAACCCT in sequence seq000240 3'-end from position 16678699
[I::telo_finder] found telo motif AAACCCT in sequence seq000250 3'-end from position 23154501
[I::telo_finder] found telo motif AAACCCT in sequence seq000260 5'-end up to position 5250
[I::telo_finder] found telo motif AAACCCT in sequence seq000270 5'-end up to position 5791
[I::telo_finder] found telo motif AAACCCT in sequence seq000280 5'-end up to position 11910
[I::telo_finder] found telo motif AAACCCT in sequence seq000290 5'-end up to position 7100
[I::telo_finder] found telo motif AAACCCT in sequence seq000290 3'-end from position 27373807
[I::telo_finder] found telo motif AAACCCT in sequence seq000300 3'-end from position 30050851
[I::telo_finder] found telo motif AAACCCT in sequence seq000310 5'-end up to position 9167
[I::telo_finder] found telo motif AAACCCT in sequence seq000310 3'-end from position 31307144
[I::telo_finder] found telo motif AAACCCT in sequence seq000320 5'-end up to position 4231
[I::telo_finder] found telo motif AAACCCT in sequence seq000320 3'-end from position 34909516
[I::telo_finder] found telo motif AAACCCT in sequence seq000330 3'-end from position 38214728
[I::telo_finder] found telo motif AAACCCT in sequence seq000340 3'-end from position 36354000
[I::telo_finder] found telo motif AAACCCT in sequence seq000710 5'-end up to position 8531
[I::telo_finder] found telo motif AAACCCT in sequence seq000720 3'-end from position 6636634
[I::telo_finder] found telo motif AAACCCT in sequence seq000730 5'-end up to position 5479
[I::telo_finder] found telo motif AAACCCT in sequence seq000730 3'-end from position 27412481
[I::telo_finder] found telo motif AAACCCT in sequence seq000740 3'-end from position 25091823
[I::telo_finder] found telo motif AAACCCT in sequence seq000760 3'-end from position 25855701
[I::telo_finder] found telo motif AAACCCT in sequence seq000770 3'-end from position 23942006
[I::telo_finder] found telo motif AAACCCT in sequence seq000780 5'-end up to position 5601
[I::telo_finder] found telo motif AAACCCT in sequence seq000800 5'-end up to position 8890
[I::telo_finder] found telo motif AAACCCT in sequence seq000810 3'-end from position 18614884
[I::telo_finder] found telo motif AAACCCT in sequence seq000820 5'-end up to position 9018
[I::telo_finder] found telo motif AAACCCT in sequence seq000850 5'-end up to position 11955
[I::telo_finder] found telo motif AAACCCT in sequence seq000850 3'-end from position 41775660
[I::telo_finder] found telo motif AAACCCT in sequence seq000860 3'-end from position 32664061
[I::telo_finder] found telo motif AAACCCT in sequence seq000870 3'-end from position 35602130
[I::main] dump hic links (BAM) to binary file yahs.out.bin
Segmentation fault (core dumped)
How to resolve the issue in order to get final high quality scaffolding genome?