MissingOutputException and latency-wait error with snakemake - snakemake

Question

I am trying to makeblastdb database in snakemake:
workdir: "/path/to/workdir/"
(SAMPLES,) =glob_wildcards('/path/to/workdir/{sample}.fasta')
rule all:
input:
expand("{sample}.fasta.{ext}", sample=SAMPLES, ext=["nhr", "nin", "nsq"])
rule makeblastdb:
input:
reference = "/path/to/workdir/{sample}.fasta"
output:
out = "{sample}.fasta.{ext}"
shell:
/Tools/ncbi-blast-2.9.0+/bin/makeblastdb -in {input.reference} -out {output.out} -dbtype nucl"
I get this error:
MissingOutputException in line 11:
Missing files after 10 seconds:
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
What is the problem?

Answer 1

I would touch a file when makeblastdb completes and use that file as dummy input for the rules that need the blast database. This way you let blast deal with suffixes and accessory files. E.g.
rule makeblastdb:
input:
reference = "/path/to/workdir/{sample}.fasta",
output:
done = touch("{sample}.makeblastdb.done"),
shell:
r"""
/Tools/ncbi-blast-2.9.0+/bin/makeblastdb -in {input.reference} -out {wildcards.sample} -dbtype nucl"
"""
rule blast:
input:
db_done= "{sample}.makeblastdb.done",
...
output:
...
shell:
r"""
blast -db {wildcards.sample} ...
"""

Answer 2

As you point out in the comments, you do not know how many files you get as output. There are two options:
Make use of output directories.
Make use of checkpoints, however this is kinda tricky to properly understand (in my opinion).
Untested but might just work:
rule makeblastdb:
input:
reference = "/path/to/workdir/{sample}.fasta"
output:
out = "{sample}.fasta.{ext}"
shell:
/Tools/ncbi-blast-2.9.0+/bin/makeblastdb -in {input.reference} -out {output.out} -dbtype nucl"
Here we mark the output as an output directory named sample-ext, and the output of ncbi-blast will be in this directory called sample.ext.
edit:
If we do not want all these output directories what we could do is say that we expect at least 1 output, and if that one exists we assume everything went fine:
rule makeblastdb:
input:
reference = "/path/to/workdir/{sample}.fasta"
output:
out = "{sample}.fasta.00.{ext}
shell:
/Tools/ncbi-blast-2.9.0+/bin/makeblastdb -in {input.reference} -out {wildcards.sample}.fasta.{wildcards.ext} -dbtype nucl"