core dumped yak qv

[skingan]

Hi, thanks for writing such a useful tool!

I am hitting a core dump when running yak qv.

$ yak version
0.1-r58-dirty

$ yak count -t 8 -o myfile.k31.yak myfile.30X.fastq
[M::worker_pipeline::0.301*3.60] processed 852 sequences; 8921223 distinct k-mers in the hash table
...
[M::worker_pipeline::76.182*4.75] processed 726 sequences; 304800752 distinct k-mers in the hash table
[M::yak_ch_dump] dumpped the hash table to file 'myfile.k31.yak'.
[M::main] Version: 0.1-r58-dirty
[M::main] CMD: yak count -t 8 -o myfile.k31.yak myfile.30X.fastq
[M::main] Real time: 92.484 sec; CPU: 377.137 sec; Peak RSS: 4.307 GB

$ yak qv -t 8 myfile.k31.yak hifiasm.asm.p_ctg.fasta > hifiasm.asm.p_ctg.k31.qv.txt
[M::yak_ch_restore_core] inserted 304800752 k-mers, of which 304800752 are new
[M::yak_qv_cb] read 358 sequences
[M::yak_qv_cb] read 0 sequences
[M::[email protected]*1.70] processed 358 sequences
[M::yak_qv_cb] read 0 sequences
yak: qv.c:232: yak_qv_solve: Assertion `adj_sum <= (double)qs->tot' failed.
Aborted (core dumped)

The input fastq file is here. Assembly file is here.

Thank you,
Sarah

[rvaser]

I have the same problem on a bacterial data set. I have added if (!isnan(qs->adj_cnt[c])) before https://github.com/lh3/yak/blob/master/qv.c#L231, which outputs expected results, but I am not sure if the estimate is correct. Any thoughts?

Best regards,
Robert

[lh3]

See #8 for details. Sorry for the late response.