core dumped

[leon945945]

Encountering the error info, but I have no idea what's wrong with the fastq file.

hifiasm: Overlaps.cpp:24087: void asg_arc_rest(asg_t*, asg_t*, uint32_t, uint32_t, ma_ug_t*, kvec_asg_arc_t_warp*, ma_hit_t_alloc*, ma_sub_t*, int32_t, int32_t, int32_t, uint32_t*): Assertion `get_edge_from_source(src_e, cov, __null, max_hang, min_ovlp, rv, rw, &t)' failed.

Please give me a hand. Thanks.

[chhylp123]

Could you please show the log file?

[leon945945]

Reads has been loaded.
[M::ha_triobin_list::2.9501.00] created the hash table for read names
[M::ha_triobin_set_list::2.9761.00] flagged 107786 reads, out of 107786 lines in file 'AJTC.asm.hap1.phase.bin'
[M::ha_triobin_set_list::3.0421.00] flagged 128473 reads, out of 128473 lines in file 'AJTC.asm.hap2.phase.bin'
[M::ha_triobin_list::3.1081.00] ==> partitioned reads with external lists
Loading ma_hit_ts from disk...
ma_hit_ts has been read.
Loading ma_hit_ts from disk...
ma_hit_ts has been read.
[M::ha_assemble::8.0220.99] ==> loaded corrected reads and overlaps from disk
[M::ha_opt_update_cov_min] updated max_n_chain to 100
[M::purge_dups] homozygous read coverage threshold: 28
[M::purge_dups] purge duplication coverage threshold: 35
[M::ug_ext_gfa::] # tips::237
Writing raw unitig GFA to disk...
Writing processed unitig GFA to disk...
[M::reduce_hamming_error_adv::0.038] # inserted edges: 0, # fixed bubbles: 0
[M::adjust_utg_by_trio] primary contig coverage range: [23, infinity]
[M::recall_arcs] # transitive arcs::48
[M::recall_arcs] # new arcs::5564, # old arcs::4614
hifiasm: Overlaps.cpp:24087: void asg_arc_rest(asg_t, asg_t*, uint32_t, uint32_t, ma_ug_t*, kvec_asg_arc_t_warp*, ma_hit_t_alloc*, ma_sub_t*, int32_t, int32_t, int32_t, uint32_t*): Assertion `get_edge_from_source(src_e, cov, __null, max_hang, min_ovlp, rv, rw, &t)' failed.

Please check it.

[chhylp123]

Thanks. Is it possible that you can share the bin files with us? It would be very helpful for us figure out the issue with bin files.

[leon945945]

sample.asm.hap1.phase.bin.txt
sample.asm.hap2.phase.bin.txt

Here are the two bin files, not sure whether I share the right bin files.

[chhylp123]

Sorry for the late reply. I need *ec.bin, *ovlp.reverse.bin and *ovlp.source.bin.

[leon945945]

They are several Gb, is it convenient to upload them?

[chhylp123]

So sorry for the later reply as I missed all github issues last week :( Could you please upload them to google drive or onedrive?

[additive3]

@chhylp123
Hi Haoyu,

I have encoutered this same issue running a trio assembly for a 10Gb genome.
I can make any files/logs available if you let me know what you need.

[chhylp123]

@chhylp123 Which version are you using?

[additive3]

@chhylp123 currently using 0.19.5-r587

[chhylp123]

Could you please have a try with: https://github.com/chhylp123/hifiasm/releases/tag/0.19.7? This issue might be fixed.

[additive3]

Will do.
Can I reuse existing bin files?

[chhylp123]

Could be reuse HiFi bin files. It would be better to reproduce UL bin files.

[additive3]

Hi @chhylp123

Ok reran from scratch using 0.19.7 and failed at same point:

[M::recall_arcs] # new arcs::1186964, # old arcs::885386
hifiasm: Overlaps.cpp:26004: void asg_arc_rest(asg_t*, asg_t*, uint32_t, uint32_t, ma_ug_t*, kvec_asg_arc_t_warp*, ma_hit_t_alloc*, ma_sub_t*, int32_t, int32_t, int32_t, uint32_t*): Assertion `get_edge_from_source(src_e, cov, NULL, max_hang, min_ovlp, rv, rw, &t)' failed.

Let me know which files you want and I can make them available

[chhylp123]

Thanks! Could you please share me the bin files and UL reads? Thanks so much!

[additive3]

@chhylp123 emailed you

[chhylp123]

Could you please have a try with the current release (0.19.8-r603)? This bug should be fixed.

[chhylp123]

@additive3

[additive3]

Hi @chhylp123
Seeing additional problems with 0.19.8 in both haplotype collapse and phasing with Hi-C data.
I can share bin files for a number of assemblies

Thanks

[chhylp123]

Sorry for the late reply @additive3. Could you please share the bin files to my gmail hcheng@ds.dfci.harvard.edu
? Thank you so much.

[additive3]

No problem @chhylp123. WIll share the bins with you now.

[additive3]

Hii @chhylp123 have you managed to access the bin files?

[chhylp123]

Sorry for the delay. Will get back to you this week!

[additive3]

No problem

[afrances1]

Any update? I am running v0.19.9 and having the same issues. I can make my bin files available if you'd like