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Snakemake workflow: rna-count-salmon

This is the Snakemake workflow for RNA-Seq read count, powered by Salmon. Optional quality controls are performed by FastQC and aggregated by MultiQC

Each tool belong to their respective authors.

See wiki for more information.

Rule graph:

Workflow

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rna-count-salmon's Issues

snakemake option : --restart-times has no effect with slurm time limit error

I'm using this command to launch the pipeline

snakemake --cluster " sbatch --mem={resources.mem_mb}M --cpus-per-task={threads} --time={resources.time_min} " --use-conda --use-singularity --reason --printshellcmds --jobs 20  --restart-times 3

12 of my 16 samples failed due to slurm time limit error.

The snakemake processus never stop and new analysis with more time allocated are never launched.

Unit testing not working

I followed the wiki to perform unit tests : "Scripts embedded within this pipeline can be tested with pytest. Go within the tests sub-directory and run: make all-unit-tests".

The error returned is : make: *** Aucune règle pour fabriquer la cible « all-unit-tests ». Arrêt.

There is no makefile in the tests sub-directory.

Time limit error for salmon rule in a slurm cluster

I have tried several times to run salmon but it fails for one sample because the pipeline default time limit is too short (75 min).

  • I have removed the --time in slurm sbatch command and the job has failed again because the default queue (shortq) with 6 hours time limit is too short for my job.

  • I have tried to set a value of 30 for --attempt (~ 9 hours) and I have observed two problems :
    1. The memory is also inscreased and I don't want to increase the memory
    2. My job has been submitted to the shortq (default) instead of the mediumq and my job stays in pending state with the reason partitionTimeLimit.

permission denied when snakemake is launched

The following command doesn't work snakemake --profile .igr/profile/slurm

Here is the error returned :

Building DAG of jobs...
Creating conda environment https:/raw.githubusercontent.com/tdayris/snakemake-wrappers/Unofficial/bio/multiqc/environment.yaml...
Traceback (most recent call last):
  File "/mnt/beegfs/userdata/m_diop/conda/envs/rna-count-salmon/lib/python3.8/site-packages/snakemake/__init__.py", line 626, in snakemake
    success = workflow.execute(
  File "/mnt/beegfs/userdata/m_diop/conda/envs/rna-count-salmon/lib/python3.8/site-packages/snakemake/workflow.py", line 836, in execute
    dag.create_conda_envs(
  File "/mnt/beegfs/userdata/m_diop/conda/envs/rna-count-salmon/lib/python3.8/site-packages/snakemake/dag.py", line 275, in create_conda_envs
    env.create(dryrun)
  File "/mnt/beegfs/userdata/m_diop/conda/envs/rna-count-salmon/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 256, in create
    os.makedirs(env_path, exist_ok=True)
  File "/mnt/beegfs/userdata/m_diop/conda/envs/rna-count-salmon/lib/python3.8/os.py", line 223, in makedirs
    mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/mnt/beegfs/pipelines/rna-count-salmon/conda/42fd2856'

Unit testing not working on a slurm cluster

I'm working on a SLURM cluster and it doesn't work. The make command was executed in the root directory that contains the Makefile.

(rna-count-salmon) [user@flamingo rna-count-salmon]$ make all-unit-tests
source $(conda info --base)/etc/profile.d/conda.sh ; conda activate ; conda activate rna-count-salmon && \
pytest -vv scripts/prepare_config.py scripts/prepare_design.py scripts/common_script_rna_count_salmon.py
bash: ligne 0 : bash: source $(conda info --base)/etc/profile.d/conda.sh ; conda activate ; conda activate rna-count-salmon && \
pytest -vv scripts/prepare_config.py scripts/prepare_design.py scripts/common_script_rna_count_salmon.py : nom d'option non valable
make: *** [all-unit-tests] Erreur 2

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