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.
Snakemake workflow for Salmon quantification and FastQC quality controls
License: GNU General Public License v3.0
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'
The pipeline has been launched on a slurm cluster with the command line specified here in the documentation : https://github.com/tdayris-perso/rna-count-salmon/wiki/Usage#slurm .
The following error occurred :
snakemake: error: ambiguous option: --singularity could match --singularity-prefix, --singularity-args
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
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.
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
.
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.
When I use the snakemake profile described here : .igr/profile/slurm
, all my jobs are executed on the master node.
Can you help me with this problem ?
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