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ChaissonLab / danbing-tk

Toolkit for VNTR genotyping and repeat-pan genome graph construction
BSD 3-Clause "New" or "Revised" License
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Assertion `its.size()' failed error in danbing-tk align #21

Closed Skye722 closed 1 year ago

Skye722 commented 2 years ago

Hi,

When testing a sample from the 1000 Genomes Project using danbing-tk align module, I encountered the error message:

danbing-tk: src/aQueryFasta_thread.cpp:128: void countDupRemove(std::vector<std::detail::_Node_iterator<std::pair<const long unsigned int, long unsigned int>, false, false> >&, std::vector<std::detail::_Node_iterator<std::pair<const long unsigned int, long unsigned int>, false, false> >&, std::vector<std::pair<unsigned char, unsigned char> >&): Assertion `its.size()' failed.

The commend I used is as follow: samtools fasta -n HG00096.bam |./danbing-tk -gc 80 -ae -kf 4 0 -cth 45 -o test -k 21 -qs pan -fai /dev/stdin -p 2 |gzip >test.aln.gz

The complete log is pleased to be provided if you need.

Thank you for helping me out!

Best, Skye

maryamghr commented 1 year ago

Hi,

I have faced exactly the same error. Could you figure out the reason for this error?

Bests, Maryam

joyeuxnoel8 commented 1 year ago

Hi all,

Sorry for the huge delay. Could you try -kf 4 1 instead? The program currently works only with the kmer filter (kf) turned on (the second integer has to be greater than 0). Let me know if you still run into any issues. Thanks!

-Tony

Skye722 commented 1 year ago

Yeah, it works with -kf 4 1. Thanks a lot!