# Snippy at Galaxy server fails to call SNPs from Fasta contigs **URL:** \ **Category:** usegalaxy.org support\ **Tags:** variant-analysis, snpeff\ **Created:** [February 10, 2020, 3:59pm UTC](https://help.galaxyproject.org/t/snippy-at-galaxy-server-fails-to-call-snps-from-fasta-contigs/2957 "2020-02-10T15:59:24Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![davitero](https://avatars.discourse-cdn.com/v4/letter/d/ecc23a/32.png) [@davitero](https://help.galaxyproject.org/u/davitero)\ **Post date:** [February 10, 2020, 3:59pm UTC](https://help.galaxyproject.org/t/snippy-at-galaxy-server-fails-to-call-snps-from-fasta-contigs/2957/1 "2020-02-10T15:59:24Z")
Dear Galaxy community, I am new in Galaxy. I am trying to call SNPs by using Snippy available at Galaxy server ([https://usegalaxy.org/](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](https://github.com/tseemann/snippy)) 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](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. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [February 10, 2020, 4:04pm UTC](https://help.galaxyproject.org/t/snippy-at-galaxy-server-fails-to-call-snps-from-fasta-contigs/2957/2 "2020-02-10T16:04:03Z")
> [@davitero](#): > > [20:25:50] Need samtools --version \>= 1.7 but you have 1.10 - please upgrade it. Hello, This is a known server-side dependency issue that we are working to correct. More feedback once done. Thanks for reporting the problem! cc @nate ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [February 10, 2020, 9:05pm UTC](https://help.galaxyproject.org/t/snippy-at-galaxy-server-fails-to-call-snps-from-fasta-contigs/2957/3 "2020-02-10T21:05:23Z")
**Update:** Tracking ticket for fix [https://github.com/galaxyproject/usegalaxy-playbook/issues/283](https://github.com/galaxyproject/usegalaxy-playbook/issues/283) ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [December 22, 2023, 12:20am UTC](https://help.galaxyproject.org/t/snippy-at-galaxy-server-fails-to-call-snps-from-fasta-contigs/2957/4 "2023-12-22T00:20:20Z")
Closed on December 22, 2023, 12:20am UTC