snippy
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tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Hi, Torsten, I am trying to use --mask option on snippy-clean_full_aln core.full.aln > clean.full.aln step for masking phage regions: snippy-clean_full_aln core.full.aln --mask PHASTER/phaster.bed> clean.full.aln and getting a following error: Unknown...
Hello, I am trying to run snippy-multi on a MacBook Pro M2 and am running into an error. Here is the snps log output: ### cd /Users/jennifercalawa/Desktop/FASTAforRoary/FNAonly ### /Users/jennifercalawa/anaconda3/envs/snippyenv/bin/snippy --outdir...
Hello, just trying to install snippy, but there is a problem. When I check snps.log, told me this: ### echo snippy 4.5.0 ### cd /home/carlosfreytas ### /home/carlosfreytas/miniconda3/envs/snippy_env/bin/snippy --cpus 8 --outdir...
Hello, I've noticed this issue in a previous post, but what worked for that individual does not seem to be working for me. I am running macOS Monterey v12.5 on...
Hi, i am trying to run snippy on multiple genomes, however it gives following error like **Please supply a reference FASTA/GBK/EMBL file with **--reference**** even after providing the reference file....
snippy looks unmaintained. Even so, it is used and we want it in Debian and GNU Guix. This issue is to track patching the software for these distros.
Dear all, I'm having some problems with the --targets argument and I don't know how to solve it: ``` Error: signal 11: freebayes(+0xbd51b)[0x7f7c18fe551b] /lib64/libc.so.6(+0x35670)[0x7f7c182a6670] /mnt/data-netapp/users/mlara/envs/snippy/bin/../lib/libstdc++.so.6(+0xd7ce7)[0x7f7c18a0bce7] /mnt/data-netapp/users/mlara/envs/snippy/bin/../lib/libstdc++.so.6(_ZNKSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE17find_first_not_ofEPKcmm+0x33)[0x7f7c18a3b913] freebayes(+0x7f1ab)[0x7f7c18fa71ab] freebayes(+0x1cede)[0x7f7c18f44ede] freebayes(+0x5f706)[0x7f7c18f87706] freebayes(+0x69103)[0x7f7c18f91103]...
~ Hi, it's my first time here. I'm trying to run Snippy for the first time with the following script: snippy-multi ../pwd_assembly --ref ../sequence.fasta --outdir snippy_analise --cpus 16 ~ But...
## Greetings! Thank you for developing Snippy! I'm a big fan of it. I recently noticed some interesting indels in my sequences. Snippy is able to detect them and store...
Hello tseemann, I am a student, doing small review on snippy. I took fastq files for one sample to compare with reference genome but when I run snippy I got...
