jia-wu-feng

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Is it necessary for --anno 1 for pangenome in the initial annotation?

Hi shujun, When closed --anno, I also got the library in *.mod.EDTA.final I don't have --curatedlib, so I just use this software results. for *.EDTA.TElib.fa, is it different? Thanks.

Is it necessary for --anno 1 for pangenome in the initial annotation?

Hi, shujun, I am sorry for my expression. My command: EDTA.pl --genome FB19_011_3_pseudomolecules_v6_hap1.fasta.1.contig.fa -t 28 --cds HBULBOSUM.r1.pgsb.Dec2021.high.cds.fa --anno 1 The results of EDTA When I don't use --curatedlib, EDTA doesn't...

minimap2: align.c:125: mm_fix_cigar: Assertion `qoff == r->qe - r->qs && toff == r->re - r->rs' failed.

Version: 2.24-r1122, The sequences are 2 big genomes(more than 3Gb). I succeed to run without -c. minimap -t 50 -2 -I 6G -K 5G -f 0.005 -x asm5 -c $ref...

minimap2: align.c:125: mm_fix_cigar: Assertion `qoff == r->qe - r->qs && toff == r->re - r->rs' failed.

Could you provide an email? And I can share this genome sequence with you. @lh3

minimap2: align.c:125: mm_fix_cigar: Assertion `qoff == r->qe - r->qs && toff == r->re - r->rs' failed.

Hi, heng I roughly know the reason, this chromosome is assembled after phasing (500MB), maybe 490MB is the same, it should be that some values are too large when outputting...

minimap2: align.c:125: mm_fix_cigar: Assertion `qoff == r->qe - r->qs && toff == r->re - r->rs' failed.

> I split my fasta into 2 parts, it will be working. Or you can use wfmash (https://github.com/waveygang/wfmash).