Error in Freebayes


I have been attempting to identify polymorphic DNA sites according to this workflow:

I am trying to use Freebayes to identify polymorphic sites from the SAM file that I cleaned up. However, I keep getting an “unable to find FASTA index” error irrespective of the version I use. Any feedback would be helpful. Thanks!

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Hi and welcome,

one suggestion first: it is way more helpful if, for reporting errors, you click on that little bug icon on the failed datset and copy/paste the complete error message you find there, instead of posting screenshots.

Now for your actual issue: the error is not about a missing FASTA index, but about specific entries in there. In other words, one or more of the chromosome names listed in your SAM/BAM inputs could not be found in the reference genome you’ve been trying to call variants against.
For your dataset 31 that makes lots of sense since Group1 is most definitely not a chromosome identifier anywhere. For dataset 32, the name is cut off in the screenshot, but it is up to you anyway to check whether this is a valid chromosome name in your analysis.

Best wishes,


That makes sense. Thanks!

Thank you for these comments. I am currently doing this project and getting the same error message.
does that mean I can continue to VCF filter even with the error message or how can I deal with that?
I will really appreciate your input in order for me to pass on this project.

Please how did you resolve the error problem?