error: update_rovlp_chain_qse

[fergsc]

Hi,
I am trying to assemble a plant genome using HiFi + ONT data. We have been sucessful using HiFiAsm on th HiFi reads alone, but when the ONT data is included we get the following error.

Input data:
hifi = 30.28 Gbp = 54.05x
ONT = 32.67 Gbp = 58.35x

Genome size: 560 Mbp

command

hifiasm                    \
    -t 48                     \
    --ul ONT.fastq.gz \
    hifi.fastq.gz

hifiasm: inter.cpp:15304: void update_rovlp_chain_qse(ma_ug_t*, int64_t, int64_t, mg_lchain_t*, int64_t, int64_t): Assertion `a[i].qs >= 0 && a[i].qs <= qlen' failed.

hifiasm.log

Thanks.

[chhylp123]

Which version are you using? Is it possible that you can share the bin files and UL reads with me? I could do a very quick check. Thanks.

[fergsc]

I have emailed you a link to the ONT UL and bin files.
I am using HiFiAsm version 0.19.6-r595

Thanks for looking in to this.

[chhylp123]

Thanks. I just had a try with your bin files and UL reads using the github HEAD (0.19.6-r597). Hifiasm could produce final contigs without issues. Could you please have a try with current HEAD? Thanks so much!

[fergsc]

Success.
I also ran it with additional UL and with Hi-C data and it ran till completion.

Thanks for the help.

[chhylp123]

Great. Thanks for the updates.