AnchorWave

AnchorWave copied to clipboard

proali Error “line 22: 54565 Killed "${EXE}_avx512" "$@"”

1

Hi, Dr Song, Thanks for your great software, firstly. Command“anchorwave proali -i xx.gff -as xx.cds.fa -r xx.fa -a xx.cds.sam -ar xx.ref.sam -s yy.fasta -n anchors -R 1 -Q 2 -o...

mushroomOK

How to combine the pairwise alignments into multiple sequence alignments？

4

@baoxingsong Hello！ I'm pleased to have a seamless experience with your software, but I do have some queries while using it. How can I utilize pairwise alignments to achieve multiple...

socialhang

Empty CDS file from gff2seq

7

Hello, I am getting an empty CDS file from running gff2seq with no error message. My command is `anchorwave gff2seq -i GCF_003119195.2_ASM311919v2_genomic.gff -r GCF_003119195.2_ASM311919v2_genomic.fna -o cds.fa` The genomic data is...

nwespe

Can AnchorWave be used for calculating identities of pairwise alignments in whole genome comparisons?

1

Dear AnchorWave team, I am currently working on a project that involves calculating identities of 1M window size pairwise alignments in whole genome comparisons. I understand that AnchorWave is designed...

cjchen5

Matching sequences align as 2 indels in paf CIGAR string

13

Hi, I'm observing an apparent bug in which AnchorWave produces paf output with a CIGAR string that reports perfectly matching sequences as containing a matching insertion and deletion. For example,...

JingaJenga

syncmers?

1

Hi, I was wondering if you considered using syncmers (I believe it's already implemented in minimap2) to map the genes between different species? I believe synmcers are specifically meant for...

cnk113

The problem of 'anchorwave proali'

5

Thank you for the development of the software Anchorwave! Here I have some problems. I now want to use anchorwave to align my assembled contigs to the reference genome. I...

xuxingyubio

Error: could not get output VCF file

3

Hi, Dr. Song Thank you for the development of the software anchorwav！I used your software to successfully generate the maf file, such as ler.anchors,ler.f.maf,ler.log,ler.maf, but unfortunately did not get the...

Bank-tidy

Error: could not parse the input VCF

1

Hi, Dr. Song I successfully generated alignment.maf using AnchorWave and converted it into a BAM file using the provided script. However, when I attempted to convert the BAM file to...

wangzhx36

there is no match anchor found in the input sam file

8

Hi, I'm trying to run AnchorWave on a pair of non-plant genomes. Whether I use minimap2 or gmap when I run the `anchorwave genoAli` function I see the following: ```...

peterdfields