# \#snippy
**URL:** https://help.galaxyproject.org/tag/snippy/464.md
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## [Snippy 4.6.0 contig-mode job intermittently fails with samtools sort -m 0M](https://help.galaxyproject.org/t/snippy-4-6-0-contig-mode-job-intermittently-fails-with-samtools-sort-m-0m/17759)
**Author:** [@dip](https://help.galaxyproject.org/u/dip)\
**Replies:** 1\
**Last updated:** [May 30, 2026, 6:35am UTC](https://help.galaxyproject.org/t/snippy-4-6-0-contig-mode-job-intermittently-fails-with-samtools-sort-m-0m/17759 "2026-05-30T06:35:37Z")
Hello Galaxy community, I am running Snippy 4.6.0 in Galaxy using assembled bacterial genome contigs as input. I am using contig mode with one FASTA genome as the reference and another assembled FASTA genome as the quer…
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## [Need help running snippy for bacterial genome](https://help.galaxyproject.org/t/need-help-running-snippy-for-bacterial-genome/17572)
**Author:** [@Sudipta\_Talukder](https://help.galaxyproject.org/u/Sudipta_Talukder)\
**Replies:** 2\
**Last updated:** [March 17, 2026, 2:34am UTC](https://help.galaxyproject.org/t/need-help-running-snippy-for-bacterial-genome/17572 "2026-03-17T02:34:11Z")
I am running snippy for the E. coli sequences using one of my isolates as reference. Was able to do some but for some getting this error “ Fatal error: Exit code 2 ()”. I’d appreciate any suggestions. Possible cause it …
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## [Please help me fix the Snippy error](https://help.galaxyproject.org/t/please-help-me-fix-the-snippy-error/17514)
**Author:** [@trinhvt](https://help.galaxyproject.org/u/trinhvt)\
**Replies:** 1\
**Last updated:** [March 1, 2026, 11:40pm UTC](https://help.galaxyproject.org/t/please-help-me-fix-the-snippy-error/17514 "2026-03-01T23:40:52Z")
Dear Sir/Madam, I’m using the Snippy tool to analyze SNPs. However, despite running it many times, I keep getting the error “Exit code 2 ()”. Could you please help me or guide me on how to fix this error? Thank you ver…
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## [Variant calling using snippy](https://help.galaxyproject.org/t/variant-calling-using-snippy/15114)
**Author:** [@Megan\_Joyce](https://help.galaxyproject.org/u/Megan_Joyce)\
**Replies:** 1\
**Last updated:** [March 29, 2025, 2:23am UTC](https://help.galaxyproject.org/t/variant-calling-using-snippy/15114 "2025-03-29T02:23:56Z")
Hi all, I’m trying to do variant calling on some bacterial isolates compared to a reference. I’ve used the snippy tool and retrieved various output files. The output file of the snp table lists all the type of variants,…
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## [Troubleshooting Snippy memory allocation error](https://help.galaxyproject.org/t/troubleshooting-snippy-memory-allocation-error/14646)
**Author:** [@P.A.P\_KUMARA](https://help.galaxyproject.org/u/P.A.P_KUMARA)\
**Replies:** 1\
**Last updated:** [February 4, 2025, 9:11pm UTC](https://help.galaxyproject.org/t/troubleshooting-snippy-memory-allocation-error/14646 "2025-02-04T21:11:01Z")
I encountered an error while running Snippy with a GenBank reference and two raw reads. Any suggestions? what I should do …? Error is denote as “It used more memory than it was allocate” . (Galaxy.org)
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## [I cant visualise any data on my SNPs table](https://help.galaxyproject.org/t/i-cant-visualise-any-data-on-my-snps-table/13785)
**Author:** [@Eleana](https://help.galaxyproject.org/u/Eleana)\
**Replies:** 2\
**Last updated:** [November 7, 2024, 10:27am UTC](https://help.galaxyproject.org/t/i-cant-visualise-any-data-on-my-snps-table/13785 "2024-11-07T10:27:29Z")
Im trying to figure out why I cant see any data in the SNPs table of BL , Ive got data in my other sample, L. casei B. Longum (BL) history L. casei history Any help gratefully accepted
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## [snippy analysis on bacterial isolates](https://help.galaxyproject.org/t/snippy-analysis-on-bacterial-isolates/12940)
**Author:** [@Jonathon\_McLaughlin](https://help.galaxyproject.org/u/Jonathon_McLaughlin)\
**Replies:** 3\
**Last updated:** [July 17, 2024, 7:08pm UTC](https://help.galaxyproject.org/t/snippy-analysis-on-bacterial-isolates/12940 "2024-07-17T19:08:48Z")
I am analysing 9 bacterial isolates of acinetobacter baumannii using snippy to identify SNPs within each sequence when compared with the reference genome. I have run BLAST on these isolates against the reference genome a…