Samtools faidx can't be run in succession on two reference files?

Question

[DdogBoss]

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?

[Pierre Lindenbaum]

what were the command lines , what were the error messages ?

[DdogBoss]

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.

[Istvan Albert]

Some bioinformaticians, when confronted with a problem, think

"I know, I'll use snakemake."

Now they have two problems.

---

That being said, you have to show the rules otherwise how could people figure out what is wrong?