Samtools faidx can't be run in succession on two reference files?
I am running a snakemake pipeline, and I had two reference genomes. One with fasta extension, and the other without.
I also had two rules to index these files using samtools faidx. The first rule had the .fai file created, and the second rule did not.
Why is this?
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DdogBoss •
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I figured out the error by only using one index instead of two, but I was just wondering why that was the case that two index rules won't necessarily work.
In response to Istvan, I will post the actual rules later.
That being said, you have to show the rules otherwise how could people figure out what is wrong?