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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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asm.bp.a_ctg.gfa file (alternate contigs) is missing #118

Open agroppi opened 3 years ago

agroppi commented 3 years ago

Hi

I have used Hifiasm-0.15.2 (r334) on Hifi reads only. hifiasm -o mysample_hifi.asm -t 32 mysample_hifi.fastq.gz

Here are all the ouput files : 

KZ-150_8_hifi.asm.bp.hap1.p_ctg.gfa
KZ-150_8_hifi.asm.bp.hap1.p_ctg.lowQ.bed
KZ-150_8_hifi.asm.bp.hap1.p_ctg.noseq.gfa
KZ-150_8_hifi.asm.bp.hap2.p_ctg.gfa
KZ-150_8_hifi.asm.bp.hap2.p_ctg.lowQ.bed
KZ-150_8_hifi.asm.bp.hap2.p_ctg.noseq.gfa
KZ-150_8_hifi.asm.bp.p_ctg.gfa
KZ-150_8_hifi.asm.bp.p_ctg.lowQ.bed
KZ-150_8_hifi.asm.bp.p_ctg.noseq.gfa
KZ-150_8_hifi.asm.bp.p_utg.gfa
KZ-150_8_hifi.asm.bp.p_utg.lowQ.bed
KZ-150_8_hifi.asm.bp.p_utg.noseq.gfa
KZ-150_8_hifi.asm.bp.r_utg.gfa
KZ-150_8_hifi.asm.bp.r_utg.lowQ.bed
KZ-150_8_hifi.asm.bp.r_utg.noseq.gfa
KZ-150_8_hifi.asm.ec.bin
KZ-150_8_hifi.asm.ovlp.reverse.bin
KZ-150_8_hifi.asm.ovlp.source.bin

==> KZ-150_8_hifi.asm.bp.a_ctg.gfa file (alternate contigs) is missing

Why ?

Thanks for your help

Alexis

chhylp123 commented 3 years ago

The current version of hifiasm doesn't output a_ctg in default. To produce it, please use '--primary'.

agroppi commented 3 years ago

OK thanks ! :) But the Readme needs to be updated here : https://github.com/chhylp123/hifiasm#assembling-hifi-reads-without-additional-data-types

;)

Cheers from Bordeaux (France)

chhylp123 commented 3 years ago

Thanks a lot. I will update it later.