Snakemake benchmark error

Question

[blackadder]

Hello there!

I hope everyone is doing ok!

I am getting a weird error in snakemake and I would appreciate your input!

I have a simple rule for downloading raw reads. The rule is working unless i add the benchmark directive and I don't know why that happens!

rule download_paired_end_reads:
"""
Downloading metagenomic raw paired end reads from ENA using enaDataGet
"""
output:
    "results/paired_end/raw_reads/{paired_reads}/{paired_reads}_1.fastq.gz",
    "results/paired_end/raw_reads/{paired_reads}/{paired_reads}_2.fastq.gz"
params:
    outdir="results/paired_end/raw_reads",
    type="fastq"
benchmark:
    "results/paired_end/raw_reads/{paired_reads}/{paired_reads}.benchmark"
shell:
    """
    enaDataGet -f {params.type} -d {params.outdir} {wildcards.paired_reads}
    """

I am getting he following error:

Error in rule download_paired_end_reads:
jobid: 11
output: results/paired_end/raw_reads/SRR9178241/SRR9178241_1.fastq.gz, results/paired_end/raw_reads/SRR9178241/SRR9178241_2.fastq.gz
shell:

            enaDataGet -f fastq -d results/paired_end/raw_reads SRR9178241

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

  Shutting down, this might take some time.
  Exiting because a job execution failed. Look above for error message
  Complete log: .snakemake/log/2023-01-16T121714.053940.snakemake.log
  (base) [user@c0020]$ Checking availability of https://www.ebi.ac.uk/ena/browser/api/xml/SRR9178241
  Downloading file with md5 check:ftp.sra.ebi.ac.uk/vol1/fastq/SRR917/001/SRR9178241/SRR9178241_1.fastq.gz

Any idea?

Thank you!

Answer 1

[Jeremy Leipzig]

probably because you are trusting your executable to create a directory the benchmarking relies on. maybe add mkdir -p results/paired_end/raw_reads/{paired_reads} above the enaDataGet command