snakemake workflow to download GEOdatasets in r have error of missing output exception

I am creating a snakemake workflow to download geodatasets. However, I get the following error

```
RuleException: CalledProcessError in file /home/sara/sara/Snakefile, line 8: Command 'set -euo pipefail; Rscript --vanilla /home/sara/sara/.snakemake/scripts/tmps2lv_wlb.meta.R' returned non-zero exit status 1. 
File "/home/sara/sara/Snakefile", line 8, in __rule_download 
File"/home/sara/mambaforge/envs/snakemake/lib/python3.11/concurrent/futures/thread.py", line 58, in run Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message
```

Here is my snakemake file

configfile: "config.yml"
rule download:
    output: 
        dir= directory("/home/sara/sara/downloads/")
    params:
        sample=config["Samples"]
    script: 
        "scripts/meta.R"

Here is my config.yml

env:
            - bioconductor-oligo
            - bioconducor-GEOquery
channels:
            - conda-forge
            - bioconda
Samples:
            - "GSE6955"
            - "GSE67311"

Here is the Rscript

library(GEOquery)
getGEOSuppFiles(snakemakege@params[sample],baseDir = snakemake@output[dir])

r geoquery snakemake

• 2,266 views • link

updated 3.6 years ago by zorbax

• written 3.6 years ago by firstorthopedicdoctor •

Syntax error: getGEOSuppFiles(snakemake@params[['sample']], baseDir = snakemake@output[['dir']])

• 0 views • link

written 3.6 years ago by zorbax

Thank you, after I fixed it, I had new error message:

**MissingOutputException in rule download** in file /home/sara/sara/Snakefile, line 7:
Job 1  completed successfully, but some output files are missing. Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
GSE6955.tar
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

• 0 views • link

written 3.6 years ago by firstorthopedicdoctor •

R code is for downloading datasets from GEOdatabase, I edited snakmake file but still same error

configfile: "config.yml"
sample=config["Samples"]
rule all:
    input:
        expand("{sample}.tar",sample=config["Samples"])

rule download:
    output: 
        "{sample}.tar"
    params:
        sample=config["Samples"]
    script: 
        "scripts/meta.R"

R code

library(GEOquery)
getGEOSuppFiles(snakemake@params[['sample']])

• 0 views • link

written 3.6 years ago by firstorthopedicdoctor •

1 answer

Try this: snakemake --use-conda -s Snakemake, where the Snakefile looks like:

configfile: "config.yml"

rule all:
    input:
        expand("{sample}/{sample}_RAW.tar", sample=config["Samples"])

rule download:
    output: 
        "{sample}/{sample}_RAW.tar"
    params:
        sample="{sample}"
    conda:
        "geo.yml"
    script: 
        "scripts/meta.R"

your config.yml:

Samples:
    - "GSE6955"
    - "GSE67311"

your conda geo.yaml file:

channels:
    - conda-forge
    - bioconda

dependencies:
   - bioconductor-oligo
   - bioconductor-geoquery

Please don't cross-post your questions, or at least put the things clear at the beginning.

When your rule all input think backward to check the correct output filename.

• 0 views • link

written 3.6 years ago by zorbax