Assertion error in running hifiasm-0.19.5

[wzboy1984]

Dear author,

I encountered the following error when I tried running hifiasm-0.19.5 on a hifi+ONT dataset.
my command line is: hifiasm-0.19.5/hifiasm -o xxx -t 32 hifi.fasta.gz --ul ont.fasta.gz

...
[M::update_sg_uo::] ==> # gfa reads:1244886, # covered gfa reads:1241365
[M::ul_realignment::] ==> starting UL
[M::ha_opt_update_cov] updated max_n_chain to 250
[M::gen_cov_track::] # bases: 7670394310
[M::ha_ct_shrink::228287.92923.37] ==> counted 38262074 distinct minimizer k-mers
[M::ha_ft_ul_gen::228300.62823.37@192.603GB] ==> filtered out 38262074 k-mers occurring 32 or more times
[M::yak_count] collected 763729387 minimizers
[M::ha_pt_ul_gen::228544.31023.36] ==> counted 106893469 distinct minimizer k-mers
[M::ha_ct_shrink::228544.75823.36] ==> counted 106893469 distinct minimizer k-mers
[M::yak_count] collected 763729387 minimizers
[M::ha_pt_ul_gen::228851.31723.34] ==> indexed 763729387 positions
[M::uidx_l_build] Index has been built.
[M::uidx_write] Index has been written.
[M::ha_opt_update_cov] updated max_n_chain to 250
[M::cal_graph_ovlp_binning::994.689] ==> Qualification
[M::write_emask_t] Index has been written.
[M::rescall_ul_pipeline::52273.014] ==> Qualification
[M::rescall_ul_pipeline::] ==> # reads: 564404, # bases: 0, # fully corrected reads: 539820
[M::write_all_ul_t] Index has been written.
hifiasm: inter.cpp:17944: void filter_short_ulalignments(void, long int, int): Assertion `a[p->aidx].pidx == (uint32_t)k' failed.

I also tried running the lastest master version with same parameters, keeping the previous generated middle files. And I got the same error message.
What should I do to avoid this error?
Looking forward to your reply.
Best wishes,

[ptrebert]

confirmed, same error here

[chhylp123]

Sorry for the late reply. Would any of you share the bin files with me? I guess it should be a small bug. Thanks in advance.

[wzboy1984]

This assertion error could be avoid by changing the aidx, pidx, etc back to -1.

[ptrebert]

@chhylp123
I am not sure I fully understand the suggested solution. In principle, I could share the BIN files via Globus if needed

[chhylp123]

Hi @ptrebert, could you please share the bin files with me? Thanks again.

[chhylp123]

This assertion error could be avoid by changing the aidx, pidx, etc back to -1.

Sorry could you please let me know what are the aidx and pidx? That would be very helpful.

[ptrebert]

@chhylp123 I prepared a Globus share, can you remind me of your globus id?

[chhylp123]

@ptrebert I was using: hcheng@jimmy.harvard.edu. Thanks a lot.

[ptrebert]

Globus doesn't find user under that email? But I used it anyway for now, hope it's the right one ...

[chhylp123]

@wzboy1984 @ptrebert Could you please have a try with current github HEAD (0.19.5-r593) using the bin files? Thanks in advance.

[alex-kozik]

Confirmed. The same error:

$ hifiasm_0.19.5 -v
0.19.5-r587

[M::rescall_ul_pipeline::] ==> # reads: 1572170, # bases: 0, # fully corrected reads: 1482668
[M::write_all_ul_t] Index has been written.
hifiasm_0.19.5: inter.cpp:17944: void filter_short_ulalignments(void*, long int, int): Assertion `a[p->aidx].pidx == (uint32_t)k' failed.

I will check 0.19.5-r593 as you (chhylp123) suggested.

[chhylp123]

Thanks. Hope the r593 works.

[alex-kozik]

@chhylp123 Thank you.
0.19.5-r593 worked without issues on the same dataset which caused job termination with 0.19.5-r587

[chhylp123]

Got it. Thanks for sharing the results!

[ptrebert]

@alex-kozik thanks for testing; sorry, I just didn't get to that in time