Dear Galaxy community,
I am new in Galaxy. I am trying to call SNPs by using Snippy available at Galaxy server (https://usegalaxy.org/).
My inputs are WGS contigs dowloaded from NCBI, not NGS reads. I have read the documentation of Snippy (GitHub - tseemann/snippy: ✂ Rapid haploid variant calling and core genome alignment) and indeed it is possible to call SNPs from WGS contigs sequences.
However, the following 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 GitHub - tseemann/snippy: ✂ Rapid haploid variant calling and core genome alignment
[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.