<p>As mentioned in a comment, your working directory lacks the fasta file.</p>

CC BY-SA 4.0
2020-06-09T21:30:32.853Z
2020-06-09T21:30:32.853Z
Devon Ryan
<p>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 <code>kallisto index -i DI_mRNA.index DI_mRNA.fa.gz</code>, there is an error saying <code>Error: FASTA file not found DI_mRNA.fa.gz</code></p>

CC BY-SA 4.0
2020-06-09T18:53:23.943Z
In what way are you running Kallisto on R?  

My guess would be you are not in the same directory as the fastq file. You can find out the current working directory with ```getwd()``` and set it with ```setwd()```.
TW93
<kallisto>
Error: FASTA file not found using building kallisto index
# Error: FASTA file not found using building kallisto index

(Asked by: username_0 on 2020-06-09)

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`

**Tags:** kallisto
> **Comments:**
> **username_1**: In what way are you running Kallisto on R?    My guess would be you are not in the same directory as the fastq file. You can find out the current working directory with ```getwd()``` and set it with ```setwd()```.  

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## 1 answers

### Answer by username_2 on 2020-06-09. Score: 2

As mentioned in a comment, your working directory lacks the fasta file.


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