Bonjour,
Je ne parviens pas à faire tourner mon script pour pyscenic du fait apparemment d un souci de compatibilite avec un package python (?).
Ci dessous la sortie d erreur lorsque je fais tourner mon script:
sbatch -A schscagingsex pyscenic.sbatch
/shared/ifbstor1/software/miniconda/envs/pyscenic-0.10.0/lib/python3.6/site-packages/dask/config.py:161: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
data = yaml.load(f.read()) or {}
/shared/ifbstor1/software/miniconda/envs/pyscenic-0.10.0/lib/python3.6/site-packages/dask/dataframe/utils.py:13: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
import pandas.util.testing as tm
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/pyscenic-0.10.0/bin/pyscenic", line 5, in <module>
from pyscenic.cli.pyscenic import main
File "/shared/ifbstor1/software/miniconda/envs/pyscenic-0.10.0/lib/python3.6/site-packages/pyscenic/cli/pyscenic.py", line 20, in <module>
from pyscenic.rnkdb import opendb, RankingDatabase
File "/shared/ifbstor1/software/miniconda/envs/pyscenic-0.10.0/lib/python3.6/site-packages/pyscenic/rnkdb.py", line 12, in <module>
from pyarrow.feather import write_feather, FeatherReader
ImportError: cannot import name 'FeatherReader'
Et ci dessous le script pyscenic.sbatch en question:
#!/bin/bash
#Options SBATCH :
#SBATCH --job-name=pyscenicOF
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=6
#SBATCH --partition=fast
#SBATCH --mem=64GB
#SBATCH -o slurm.%N.%j.out
#SBATCH -e slurm.%N.%j.err
module load pyscenic/0.10.0
PATHproject="/shared/projects/schscagingsex/pyscenic/"
suffix="OF"
i=1
pyscenic grn ${PATHproject}expressionRawCount${suffix}ForScenic.tsv ${PATHproject}mm_mgi_tfs.txt -o ${PATHproject}GRNboost/GRNboost${suffix}_${i}.tsv --seed ${i}
Merci beaucoup!
Claire