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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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line 8: 110334 Aborted(core dumped) #642

Open yao-chenxin opened 5 months ago

yao-chenxin commented 5 months ago

Hello, I have a hypermemory problem: The error message is as follows:

[M::ha_hist_line] rest: ****> 50214823 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: none [M::ha_ft_gen] peak_hom: 53; peak_het: -1 [M::ha_ct_shrink::20212.2275.86] ==> counted 73802001 distinct minimizer k-mers [M::ha_ft_gen::20288.5855.84@59.941GB] ==> filtered out 73802001 k-mers occurring 265 or more times [M::ha_opt_update_cov] updated max_n_chain to 265 [M::yak_count] collected 1223402570 minimizers [M::yak_count] collected 1637002108 minimizers [M::yak_count] collected 439807275 minimizers [M::yak_count] collected 1693570594 minimizers [M::yak_count] collected 434857897 minimizers [M::yak_count] collected 182925201 minimizers hifiasm: sketch.cpp:581: void mz1_ha_sketch(const char, int, int, int, uint32_t, int, ha_mz1_v, const void, int, kvec_t_u8_warp, kvec_t_u64_warp, ha_pt_t, int, int32_t, float, st_mt_t, int32_t, int32_t, void): Assertion len > 0 && (int64_t)(len) < (int64_t)((((uint64_t)1)<<27)) && (int64_t)(rid) < (int64_t)((((uint64_t)1)<<28)) && (w > 0 && w < 256) && (k > 0 && k <= 63)' failed. /opt/ge2011.11/default/spool/compute01/job_scripts/2912: line 8: 110334 Aborted (core dumped) /software/hifiasm-0.19.8/hifiasm -o $spe -t 20 --hom-cov 53ls *.fasta.gz` ERROR: failed to read the graph no sca ERROR: failed to read the graph

My memory is given 1.5T (vg=1.5T,p=35),still can't solve; Could you please take a look? Is there any good solution.(The genome is 9 g)（--hg-size 9g） Thank you very much！

chhylp123 commented 5 months ago

@yao-chenxin Sorry for the late reply. I feel like the issue might be caused by non-ACGT base pairs within input HiFi reads.

RiversDong commented 2 months ago

How to solve this error?

yao-chenxin commented 2 months ago

hi,

I checked and found that there was an incomplete fastq file, re-generated fastq with bam2fastq, and then fixed the problem.

Best wishes!

在 2024-07-23 08:27:15，"Chuan Dong" @.***> 写道：

How to solve this error?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

RiversDong commented 2 months ago

hi, I checked and found that there was an incomplete fastq file, re-generated fastq with bam2fastq, and then fixed the problem. Best wishes! 在 2024-07-23 08:27:15，"Chuan Dong" @.> 写道： How to solve this error? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.>

Thank you for your kind response. I will try this solution and provide you with my feedback. Best wishes.