Comments (4)
With minimap2, you need to add option -I60g
.
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By the way, our latest version should be better than v0.8. The latest version can avoid some misassemblies. If you have v0.8 bin files, it is quite fast to rerun v0.11.
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@lh3 I try to add the option -I60g. Unfortunately, now the max RAM of my cluster is 256G, and it is not enough to index the genome, so can you give me some advices to reduce the required RAM?
@chhylp123 Thank you very much for your advice! Yeah, I have v0.8 bin files and I have tried to use the v0.11 to rerun it, however the required RAM also exceeds 256G.
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256G is too small for redwood. Hifiasm needs about 700Gb RAM in this case.
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Related Issues (20)
- Possible missing one haplotype in human assemblies HOT 2
- No haploid.gfa files output in trio-binning mode HOT 3
- Hifi + Hi-c + ONT assembly fails
- In Trio-binning, always more on hap1 despite (almost) same sequences for paternal and maternal
- discontinuous assembly with shorter pacbio hifi reads but high coverage HOT 2
- Is x20 of Hifi data enough to construct draft assembly of 6.5Gb genome? HOT 1
- line 8: 110334 Aborted(core dumped) HOT 1
- Ultra Long intergration failed: no output for UL kmer counting HOT 3
- missing 8Mb sequences in the assembly HOT 5
- Empty haplotype 2 gfa files by ONT integration HOT 1
- Basic Question About HiFi Input HOT 3
- Spend too long times to run hifiasm HOT 1
- Switch error on X and Y chromosome HOT 2
- *.ovlp.bin file HOT 1
- Resolving switching error (?)
- Interchromosomal misjoin HOT 1
- Read error correction does not reduce the number of kmers present once, twice or three times
- Recreate p_ctg from p_utg
- In the diploid assembly, hfiiasm identified a value that did not exist in the k-mer plot as the "homozygous read coverage threshold".
- fungi diploid assemble phasing errors
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