Slugger70
commented
4 years ago What can we do in the mean time?
Open davitero opened 4 years ago
Slugger70
commented
4 years ago What can we do in the mean time?
davitero
commented
4 years ago Hi @Slugger70
I have no problem to perform snippy analysis using as input NGS sequence reads. However, when the inputs are complete or draft genomes download from NCBI, then snippy fails to call SNPs.
Please see this share history for more details.
https://usegalaxy.eu/u/davitero/h/e-coli-snps
4: snippy on data 1 snps table. 1 line, 0 SNPs identified
15: snippy on data 11 and data 12 snps table. 78,562 lines, 78,562 SNPs identified
mattbawn
commented
1 year ago Hi @tseemann is there a way to use variant call from contigs/assemblies using Snippy on Galaxy at the moment?
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 2 ()"
I appreciate any help with this problem.
Tool generated the following standard error: [20:25:49] This is snippy 4.4.5 [20:25:49] Written by Torsten Seemann [20:25:49] Obtained from https://github.com/tseemann/snippy [20:25:49] Detected operating system: linux [20:25:49] Enabling bundled linux tools. [20:25:49] Found bwa - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/bwa [20:25:49] Found bcftools - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/bcftools [20:25:49] Found samtools - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/samtools [20:25:49] Found java - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/java [20:25:49] Found snpEff - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/snpEff [20:25:49] Found samclip - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/samclip [20:25:49] Found seqtk - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/seqtk [20:25:49] Found parallel - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/parallel [20:25:49] Found freebayes - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/freebayes [20:25:49] Found freebayes-parallel - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/freebayes-parallel [20:25:49] Found fasta_generate_regions.py - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/fasta_generate_regions.py [20:25:49] Found vcfstreamsort - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/vcfstreamsort [20:25:49] Found vcfuniq - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/vcfuniq [20:25:49] Found vcffirstheader - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/vcffirstheader [20:25:49] Found gzip - /bin/gzip [20:25:49] Found vt - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/vt [20:25:49] Found snippy-vcf_to_tab - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/snippy-vcf_to_tab [20:25:49] Found snippy-vcf_report - /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-8b12e3c0ffd8bb115bc7f1ba98dc3e6f2437163780e6bedf407dfe51c8fc8d1e/bin/snippy-vcf_report [20:25:50] Need samtools --version >= 1.7 but you have 1.10 - please upgrade it.