ChaissonLab / danbing-tk

Toolkit for VNTR genotyping and repeat-pan genome graph construction

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danbingtk v1.3.2 align error

ghzhaole opened this issue · comments

Hi,
When I test the "align" module of danbing-tk v1.3.2, there were errors occurred.
when using the command:
danbing-tk -gc 85 -ae -kf 4 1 -cth 45 -o $sample -k 21 -qs pan -fa $WORKDIR/${sample}.fasta -p 16
the error was:

[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 730496712 reads
use baitDB: 0
extract fasta: 0
interleaved: 0
sim mode: 0
trim mode: 0
augmentation mode: 0
graph threading mode: 1
output alignment: 1
output successfully aligned reads only: 1
k: 21
# of subsampled kmers in pre-filtering: 4
minimal # of matches in pre-filtering: 1
Cthreshold: 45
Rthreshold: 0.5
threading Cthreshold: 85
Running both step1 (kmer-based filtering) and step2 (threading)
fastx: /shared/home/zhangsj/scripts/danbingtk-1.3.2/HG00405.fasta
query: pan.(tr/ntr).kmers

total number of loci in pan.tr.kmers: 80517
deserializing kmerDBi.umap
deserializing kmerDBi.vv
deserializing graph.umap
reading kmers from pan.tr.kmers
terminate called after throwing an instance of 'std::out_of_range'
  what():  stoul
Aborted (core dumped)

when using the command:
danbing-tk -gc 85 3 -ae -kf 4 1 -cth 45 -o $sample -k 21 -qs pan -fa $WORKDIR/${sample}.fasta -p 16
the error was:

[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 730496712 reads
invalid option: 3
terminate called without an active exception
Aborted (core dumped)

Could you please help me this out? Many thanks!!