Aborted run

[acdarby]

Not sure if this error is helpful! So please give me some direction on what I need to post!

[M::ha_opt_update_cov] updated max_n_chain to 100
hifiasm: inter.cpp:16098: void gen_trans_base_count_comp(ug_trans_t*, kv_u_trans_t*): Assertion `z->nw > 0' failed.
Aborted

hifiasm -o AV_2023 --h1 R1_001_sub250.fastq.gz --h2 R2_001_sub250.fastq.gz -t 36 AV.HiFi.fasta

[chhylp123]

Thanks for letting us know. This is a specific issue for 0.18.5-r499. We are trying to fix it as soon as possible. Could you please use Hifiasm-0.18.4-r496 beta or Hifiasm-0.18.2-r467 beta first? Rerun 0.18.4 or 0.18.2 could reuse existing bin files, so it shouldn't take too much time. I will let you know once this issue is fixed.

[acdarby]

ok so rolled back to Hifiasm-0.18.4-r496 beta and getting the same error using the existing bin! restart with new bin?

[chhylp123]

Can you roll back to Hifiasm-0.18.2-r467 beta or an earlier version with existing bins? I believe an eariler version could defintely work. But I will also cut a new release to fix this bug this week.

[acdarby]

Hi I had not tired to roll back because I was hoping for a new version! Should I wait or go with the roll back?
Thanks for you work on this

[chhylp123]

Sorry for the late. I will cut it tommorrow.

[chhylp123]

@acdarby Could you please rerun 0.18.5 but set --s-base to -1? It will disable the base-level alignment for homology detection. The base-level alignment part results into this issue.

[acdarby]

sure I will give it a got

[chhylp123]

Hi @acdarby, I have pushed the new version of hifiasm to the HEAD (0.18.6-r513). I think it should be able to fix the issue of HiC. Sorry for the delay.

[chhylp123]

I have cut a new release. The new release should be able to fix this issue.

[weirdo-onlooker]

Hi @chhylp123, I have met the similar problem he had , but using Hifiasm-0.19.2. My log files all end with the following content.

[M::mc_solve:: # edges: 3414]
[M::mc_solve_core_adv::0.307] ==> Partition
[M::adjust_utg_by_primary] primary contig coverage range: [31, infinity]
Writing ../hic_hifi_1/hhh_hifiasm_hic_hifi_assembly_1.hic.p_ctg.gfa to disk...
[M::ha_opt_update_cov] updated max_n_chain to 190

hifiasm -o output.prefix -t 20 --h1 HIC.R1.fastq.gz --h2 HIC.R2.fastq.gz INPUT.fasta

The task status is killed.

[weirdo-onlooker]

@chhylp123 Or can you provide me with the test data of hic ? So I can tell if there's something wrong with my data.

[chhylp123]

It seems the task was killed due to there is no enough memory. Could you set --s-base -1? This will disable the base-level homology detectio will less memory requirement.

[jsharbrough]

Hello, I'm trying to incorporate long reads into my hifi read assembly and am getting a similar error with v0.19.5-r587. This command has worked for different libraries, but not for this one. I've got access to lots of memory, but it doesn't seem to help the job finish whether I give it 239Gb (64 threads) or 1031 Gb (48 threads):

hifiasm -o hifi+CLR.asm -l0 -t48 --ul longReads.fastq.gz movie.hifi_reads.fastq.gz

tried the --s-base -1 fix, but the same error resulted:

hifiasm: inter.cpp:15977: uint32_t refine_rid_chain(const asg_t*, mg_tbuf_t*, ul_vec_t*, uint64_t): Assertion `ni[1] > ni[0] && ni[0] != (uint32_t)-1 && ni[1] != (uint32_t)-1' failed.

Assuming this is a memory issue, is there a way to limit the memory usage to the available architecture? Or estimate the amount of memory needed and provide that? Let me know if you need to see any of my .bin files

Thanks!

[eernst]

I'm seeing this same error with v0.19.5-r587 and the latest commit (30d2ee0).

--s-base -1 has no effect, and it doesn't seem memory related, don't see high memory pressure before this call on 1.5TB machine.

[chhylp123]

@eernst Is it possibe that you can share the bin files with me? I could fix this issue soon. Thanks a lot.

[chhylp123]

Could you please have a try with the latest release (0.19.6-r595)? However, polyploid assembly might still be not prefect.

[eernst]

Ran successfully! Thank you for working on this.