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snakemake-workflows / dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow
MIT License
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Failed to open environment file #19

Open CharlesJB opened 4 years ago

CharlesJB commented 4 years ago

Hello,

I cloned the dna-seq-gatk-variant-calling workflow on a cluster and I am getting the following error when I try to launch snakemake:

Building DAG of jobs...
WorkflowError:
Failed to open environment file https://github.com/snakemake/snakemake-wrappers/raw/0.30.0/bio/trimmomatic/pe/environment.yaml:
URLError: <urlopen error [Errno 110] Connection timed out>

I did the following steps:

  1. Clone the repo
  2. Filled the *.tsv files and the config file with the correct infos for the run
  3. Test using snakemake -np. Everything is OK at this step.
  4. Prepare the cluster.json file
  5. Launch snakemake:
snakemake --use-conda -k -p -j 999 --cluster-config cluster.json --cluster "sbatch -A {cluster.account} -t {cluster.time} --mem {cluster.mem} --cpus-per-task {cluster.cpus-per-task}"

The jobs are submitted correctly to the cluster, but they crash after a few minutes. In the logs, I find the error message I pasted at the beginning of this issue.

I was under the impression that the wrappers were downloaded before launching the jobs, but it does not appear to be the case.

I then tried to clone the snakemake-wrappers repo and link it directly with the --wrapper-prefix parameter using the git+file://path/to/your/local/clone@ as mentioned in the doc. I get the following error:

ValueError in line 12 of /lustre04/scratch/jolybeau/LO/LO_genotypage/dna-seq-gatk-variant-calling/rules/mapping.smk:
too many values to unpack (expected 2)
  File "./dna-seq-gatk-variant-calling/Snakefile", line 16, in <module>
  File "./dna-seq-gatk-variant-calling/rules/mapping.smk", line 12, in <module>

I'm not sure what I am doing wrong. Could you please help me with this problem?

Charles.