Minimap2 crash in the whole genome alignment

[xinzilan]

Hello,
I have encountered a weird issue when using minimap2 to do whole genome alignment. My data conatins a short assembly A (haplotype) and a long assembly B (diploid). When I used the assembly A as a targeted reference and aligned assembly B (query), it works well. However, when I used the assembly B as a targeted reference and aligned assembly A (query) , I encoutered an issue shown below. Does someone know the reasons?

minimap2: align.c:820: mm_align1: Assertion `qe1 <= qlen' failed.
minimap2_maf.sh: line 9: 3580123 Aborted (core dumped) minimap2 -t $5 --cs=long --secondary=no $target_ref $query_ref &gt; ${name}.paf

I also get the warning that: [WARNING] logic inconsistency in mm_est_err(). Please contact the developer.

[lh3]

What are the sequence lengths? Could you provide the sequences?

[xinzilan]

Hi, Dr. Li, Glad to hear from you. Since the fasta files are too big to upload in github, I email them. The length of assembly B (diploid) I used is 6027020623 while the length of assembly A (GRCh38) is 3099922541. The link of sequences is attached to this email https://wustl.box.com/s/nwworprzmbj8i38sjd5ta9tlu1h19udr and here is my command: minimap2 -t 15 --cs=long --secondary=no assembly_B.fasta GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta > B_hg38.paf Thanks a lot for your support!

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________________________________ 发件人: Heng Li ***@***.***> 发送时间: 2024年10月13日 23:04 收件人: lh3/minimap2 ***@***.***> 抄送: Xin, Zoulan ***@***.***>; Author ***@***.***> 主题: Re: [lh3/minimap2] Minimap2 crash in the whole genome alignment (Issue #1248) * External Email - Caution * What are the sequence lengths? Could you provide the sequences? ― Reply to this email directly, view it on GitHub<#1248 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BCAYXRJJHH2DLZ7XOXV4OVLZ3M7GPAVCNFSM6AAAAABPXPSUPOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBZHEYDCMBZGA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

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[anthonysnead]

I have been having the same issue. My two assemblies are about 2.3 Gb long. Did you all ever resolve the issue?

[miaojiashun]

Same issue, my genomes is about 4Gb.