python: ctg_cns.c:601: generate_lqseqs_from_cluster: Assertion `lqseq->start == clu->r.s' failed.

[zhangrengang]

Describe the bug I got python: ctg_cns.c:601: generate_lqseqs_from_cluster: Assertionlqseq->start == clu->r.s' failed.` and then the process was suspended. Only one contig had got the exeption and all the others are OK.

Error message

[INFO] 2020-07-23 10:31:21,483 Corrected step options:
[INFO] 2020-07-23 10:31:21,483 Namespace(alignment_identity_ratio=0.8, alignment_score_ratio=0.8, auto=True, bam_list='01_rundir/03.ctg_graph/03.ctg_cns.input.bams', block='01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nd.asm.p.fasta.blc', block_index='50', genome='01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nd.asm.p.fasta', out='nd.asm.f.part050.fasta', process=1, read_type=1, split=1, window=5000000)
[WARNING] 2020-07-23 10:31:23,435 Adjust -p from 1 to 33, -w from 5000000 to 5000000, logical CPUs:88, available RAM:~238G, use -a to disable automatic adjustment.
[INFO] 2020-07-23 10:31:23,449 Start a corrected worker in 33708 from parent 33690
[INFO] 2020-07-23 10:31:23,450 Start a corrected worker in 33711 from parent 33690
[INFO] 2020-07-23 10:31:23,450 Start a corrected worker in 33709 from parent 33690
[INFO] 2020-07-23 10:31:23,451 Start a corrected worker in 33712 from parent 33690
[INFO] 2020-07-23 10:31:23,451 Start a corrected worker in 33710 from parent 33690
[INFO] 2020-07-23 10:31:23,453 Start a corrected worker in 33713 from parent 33690
[INFO] 2020-07-23 10:31:23,455 Start a corrected worker in 33714 from parent 33690
[INFO] 2020-07-23 10:31:23,456 Start a corrected worker in 33715 from parent 33690
[INFO] 2020-07-23 10:31:23,457 Start a corrected worker in 33716 from parent 33690
[INFO] 2020-07-23 10:31:23,458 Start a corrected worker in 33718 from parent 33690
[INFO] 2020-07-23 10:31:23,458 Start a corrected worker in 33717 from parent 33690
[INFO] 2020-07-23 10:31:23,459 Start a corrected worker in 33719 from parent 33690
[INFO] 2020-07-23 10:31:23,461 Start a corrected worker in 33720 from parent 33690
[INFO] 2020-07-23 10:31:23,462 Start a corrected worker in 33721 from parent 33690
[INFO] 2020-07-23 10:31:23,463 Start a corrected worker in 33722 from parent 33690
[INFO] 2020-07-23 10:31:23,463 Start a corrected worker in 33724 from parent 33690
[INFO] 2020-07-23 10:31:23,463 Start a corrected worker in 33723 from parent 33690
[INFO] 2020-07-23 10:31:23,466 Start a corrected worker in 33726 from parent 33690
[INFO] 2020-07-23 10:31:23,466 Start a corrected worker in 33725 from parent 33690
[INFO] 2020-07-23 10:31:23,468 Start a corrected worker in 33727 from parent 33690
[INFO] 2020-07-23 10:31:23,468 Start a corrected worker in 33729 from parent 33690
[INFO] 2020-07-23 10:31:23,469 Start a corrected worker in 33728 from parent 33690
[INFO] 2020-07-23 10:31:23,469 Start a corrected worker in 33730 from parent 33690
[INFO] 2020-07-23 10:31:23,471 Start a corrected worker in 33731 from parent 33690
[INFO] 2020-07-23 10:31:23,473 Start a corrected worker in 33733 from parent 33690
[INFO] 2020-07-23 10:31:23,473 Start a corrected worker in 33732 from parent 33690
[INFO] 2020-07-23 10:31:23,475 Start a corrected worker in 33734 from parent 33690
[INFO] 2020-07-23 10:31:23,476 Start a corrected worker in 33736 from parent 33690
[INFO] 2020-07-23 10:31:23,476 Start a corrected worker in 33735 from parent 33690
[INFO] 2020-07-23 10:31:23,478 Start a corrected worker in 33737 from parent 33690
[INFO] 2020-07-23 10:31:23,479 Start a corrected worker in 33738 from parent 33690
[INFO] 2020-07-23 10:31:23,480 Start a corrected worker in 33740 from parent 33690
[INFO] 2020-07-23 10:31:23,480 Start a corrected worker in 33739 from parent 33690
gap_aln:274 sup_aln:331 depth_cluster:3 gap_cluster:2 split_count:0 bin_len:1316 median_depth:65
python: ctg_cns.c:601: generate_lqseqs_from_cluster: Assertion `lqseq->start == clu->r.s' failed.
[INFO] 2020-07-23 10:31:39,650 Start a corrected worker in 33941 from parent 33690

Genome characteristics genome size: 1.5G heterozygous rate: 1%

Input data sequencing depth:100x N50 read length: 30k

Operating system CentOS Linux release 7.7.1908 (Core)

GCC gcc version 5.4.0 (GCC)

Python Python 2.7.10

NextDenovo nextDenovo v2.3.0

[moold]

Hi, could you extract the unfinished contigs and the corresponding bam file, and send these two files to me?

[zhangrengang]

I am sorry that the bam files have been deleted by nextDenovo because I replaced the failed contig with that in 01.ctg_graph.sh.work/ctg_graph0/nd.asm.p.fasta and re-run nextDenovo.