snippy

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Hi！Torsten

TaoCheng98

error

4

I am trying Snippy with contigs genomes, but after running for a while it shows the following error. Please suggest how to improve it. Also, I tried snippy-multi but it...

sekhwal

Snippy at Galaxy server fails to find SNPs from Fasta contigs

3

Hi, I am trying to find SNPs from WGS contigs dowloaded from NCBI by using snippy available at Galaxy server (https://usegalaxy.org/). However, an error is presented: "Fatal error: Exit code...

davitero

Hi! I was calling SNPs with 30 CPUs. However, I noticed that after SNP calling, when snippy-core started, the CPU usage was of only one. Is there a way to...

Alejandro-PI

snippy core took isolate as ref

1

Hi Seeman I ran snippy on mutliple isolates with the input.tab snippy-multi input.tab --ref ../gubbins_dir/ref_seq_dir/GCF_001600975_1_ASM160097v1.fasta --cpus 16 > runme.sh When checked the file runme.sh, I noticed one of my isolates...

tbazilegith

Missing build items in conda OR freebayes-parrallel problem

2

Hello, I hope you're well. I am struggling to get any install of Snippy working. I've followed all instructions using either Conda or Brew, and both result in errors. I've...

hughgifford

Got broken pipeline when running freebayes-parallel

28

I got this error like this. Does anyone can help to fix?? I run command on HPC: snippy --R1 $p_trim/VN0467_1_paired.fastq.gz --R2 $p_trim/VN0467_2_paired.fastq.gz --outdir /lustre7/home/buihoangphuc412/Projects/GWAS/variant/VN0467 --prefix VN0467 --ref $p_ref/genome/CHC97.fasta --report --cpus...

buihoangphuc412

SNIPPY-CORE ERROR: Could not extract base XX_Referenece.1:134 for isolate XXX_out

4

Dear Tseemann, We got this unusual error when running snippy-core on the snippy output folders where it says: " ERROR: Could not extract base NZ_CP084351.1:134 for isolate AD_SRR13280317_1.fastq_out" (with NZ_CP084351...

gilmahu

Hi, I'm using snippy v4.6.0 in the --ctg contig mode. It does not detect snps at the ends of the contigs. Something seems to be wrong with the uniform coverage...

Saarkie

.gb file not working as the reference and with fasta reference, FTYPE,STRAND,NT_POS, AA_POS , EFFECT,LOCUS_TAG,GENE PRODUCT are empty columns

4

I installed snippy v 4.6.0 and snpEff version SnpEff 5.1d (build 2022-04-19 15:49). When the reference file is a .gb file, I encounter the following error [19:30:07] This is snippy...

absartalat