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Could not find .aligned.fa/.vcf in 73

9

I'm trying to run snippy-multi for a few assembled genomes. 73 /xulie/shiyanshijiyuanfenxi/jiyuanxulie/73.fasta 75 /xulie/shiyanshijiyuanfenxi/jiyuanxulie/75.fasta 95 /xulie/shiyanshijiyuanfenxi/jiyuanxulie/95.fasta A1 /xulie/shiyanshijiyuanfenxi/jiyuanxulie/A1.fasta A6 /xulie/shiyanshijiyuanfenxi/jiyuanxulie/A6.fasta D-3-11 /xulie/shiyanshijiyuanfenxi/jiyuanxulie/D-3-11.fasta snippy-multi input.tab --reference Reference.gbk > 1.sh ./1.sh The...

zhichusun

I try to use miniconda ad create a new environment install SNIPPY ,it still report "line11"error. I change my system from centos to Ubuntu.It stll report... the only I could...

Albertzhuo123

Hi, i am trying to run snippy regarding SNP analysis and it give following error, please have a look **snippy-multi /home/bvs/Neelam/annotated/fna/input.tab --reference /home/bvs/Neelam/annotated/gbk/P_aeruginosa_PAO1.gbk --cpus 16 > out** Reading: /home/bvs/Neelam/annotated/fna/input.tab ERROR:...

neelam19051

Hello, snippy was working great - I then ran `brew update` and things went downhill. This is the error (and see log): ``` Running: freebayes-parallel reference/ref.txt 8 -p 2 -P...

osekulovic

Hi, i am trying to run snippy regarding SNP analysis and it give following error, please have a look **snippy-multi /home/bvs/Neelam/annotated/fna/input.tab --reference /home/bvs/Neelam/annotated/gbk/P_aeruginosa_PAO1.gbk --cpus 16 > out** Reading: /home/bvs/Neelam/annotated/fna/input.tab ERROR:...

neelam19051

Hello I am trying to run freebayes (as part of snippy) but get this error I do have vcflib isntalled in my env /opt/miniconda3/envs/instaflu_env/bin/freebayes-parallel: line 40: 1655 Done ( cat...

antoine4ucsd

Hi, Not reporting a problem, just a comment, but perhaps someone might have a better way of going about this: Regarding the vow: "wish you a life free of homopolymer...

SantosJGND

ploidy set to 2? And failing at bcftools consensus

4

Hey, I have 2 inquiries. I am running snippy to detect variance between multiple copies of the same part of a bacterial genome. 1. I saw the log (attached) of...

Sidduppal

"ERROR: Database check failed" with snpEff and possible fix

5

Thanks for the nice software! Hopefully this is not duplicated. I got this error when trying to run snippy, installed with mamba, on a gbk reference. ``` WARNING_GENE_NOT_FOUND: Too many...

fpusan

snippy-multi - bed targets file is not open

5

Hi! Thanks for this useful program! This is the first time I use snippy-multi. This is my `input.tab` file: ``` PNG84A /media/koala/Main/mishell/snippy-multi/t1/210.2442.fna G272 /media/koala/Main/mishell/snippy-multi/t1/210.2712.fna ``` My target proteins in my...

Silverfoxcome