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tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Dear all, I have an issue when the code 'snippy -check' is performed. Here's the detail. (Below) snippy -check [01:54:34] This is snippy 4.6.0 [01:54:34] Written by Torsten Seemann [01:54:34]...
Hello! I ran snippy-multi on a dataset of about 20 bacterial isolates (*.fasta assemblies) within the same genus (_Enterobacter_ spp.). The core genome length (from core.aln) was around 273,000 base...
bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf dyld[7336]: Library not loaded: @rpath/libcrypto.3.dylib Referenced...
I get an error message when running snippy-multi for my .fastq files `ERROR: Could not find .aligned.fa/.vcf in (snippy folder)`. When I open the folder indeed .aligned.fa/.vcf is not found....
Hi, When I use snippy-core, it prints out tables like this: 0 plasmid1 snp=314 del=1 ins=4 het=3 unaligned=12667 1 palsmid2 snp=563 del=4 ins=2 het=5 unaligned=16502 2 plasmid3 snp=1261 del=21 ins=8...
Hi, I am using snippy and have snpEff 5.1d installed when installing snippy. Test run smoothly locally but error occur when submitting job to HPC using sbatch. [15:43:07] Found snpEff...
Dear all, I am running snippy core on a lot of samples (around 1000) but for processing reasons I cannot run snippy and then snippy-core on all samples at once....
[snps.log](https://github.com/tseemann/snippy/files/14536244/snps.log) I met a problem when run snippy. I think it may relate to freebayes, but I don't know how to fix. ps：snippy --check show "Dependences look good!"
Hello,I encountered the following problems when using snippy. Has anyone encountered similar problems? snippy is installed with conda. vcfstreamsort: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file:...
Running in WSL2Ubuntu. Have 227 assemblies in contigs in .fna. commands: snippy-multi files.txt --ref ../prokka227/SA1.gbk --cpus 16 > runme.sh sh ./runme.sh symptoms: completes all the calls to snippy but then...
