Snippy results in no variants (my data and microbial variant tutorial)


I’m using the Snippy tool in Galaxy for a local instance. This tools runs with no errors and exports many outputs but there is no actual data in any of them. At first, I thought this was just related to my data but then tried the sample data in the microbial variant tutorial and the same thing happened. To my knowledge, all of the inputs and parameters are in the correct format.


  • “Reference File” to the wildtype.gbk file (if the genbank file is not selectable, make sure to change its datatype to ‘genbank’)
  • “Single or Paired-end reads” to Paired
  • “Select first set of reads” to mutant_R1.fastq
  • “Select second set of reads” to mutant_R2.fastq

The result has a table with no variants listed. Here are the detailed results that came out of Galaxy…

[16:49:52] This is snippy 4.5.0
[16:49:52] Written by Torsten Seemann
[16:49:52] Obtained from
[16:49:52] Detected operating system: linux
[16:49:52] Enabling bundled linux tools.
[16:49:52] Found bwa - /opt/krb5_galaxy

No idea why it just stops there…

Thank you!!!