tdayris-perso / rna-count-salmon Goto Github PK
View Code? Open in Web Editor NEWSnakemake workflow for Salmon quantification and FastQC quality controls
License: GNU General Public License v3.0
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'
(self-explanatory title)
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.
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.
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 ?
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 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
.
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