Error: FASTA file not found using building kallisto index I am trying to build an index on kallisto on mac using R studio and have saved my FASTA file to my desktop, however, when I run kallisto index -i DI_mRNA.index DI_mRNA.fa.gz, there is an error saying Error: FASTA file not found DI_mRNA.fa.gz
As mentioned in a comment, your working directory lacks the fasta file.