Snippy at Galaxy server fails to find SNPs from Fasta contigs

[davitero]

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.