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baoxingsong / dCNS

conserved non-coding sequence
MIT License
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[multCns] dCNS multCns #30

Open ddwojius opened 8 months ago

ddwojius commented 8 months ago

Hi, @baoxingsong ! I have an error in the dCNS mult-Cns step. My running code:

dCNS multCns -i ref.genome.fa -o msa.fasta -s s1.sam s2.sam s3.sam

The sam file was from minimap2 step:

minimap2 -ax splice -a -uf -C 1 -k 12 -P -t 12 --cs Setaria_italica.Setaria_italica_v2.0.dna.toplevel.fa gene.fa > setaria.sam

The error info:

reference genome reading done
begin to read Actinidia_deliciosa.sam
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr: __pos (which is 3714269) > this->size() (which is 0)
Aborted (core dumped)

Do you know how to fix it? Thank you for your help!

ddwojius commented 8 months ago

https://github.com/baoxingsong/dCNS/issues/29