WARNING: Can't draw plots: python-matplotlib is missing or corrupted.
Reference:
/shared/ifbstor1/home/santinis/raw_data/MLC_20200107.fasta ==> MLC_20200107
Contigs:
Pre-processing...
No module named 'joblib3'
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/quast-5.0.2/opt/quast-5.0.2/quast_libs/qutils.py", line 1049, in run_parallel
import joblib
ModuleNotFoundError: No module named 'joblib'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/quast-5.0.2/bin/quast", line 307, in <module>
return_code = main(sys.argv[1:])
File "/shared/ifbstor1/software/miniconda/envs/quast-5.0.2/bin/quast", line 107, in main
contigs_fpaths, old_contigs_fpaths = qutils.correct_contigs(contigs_fpaths, corrected_dirpath, labels, reporting)
File "/shared/ifbstor1/software/miniconda/envs/quast-5.0.2/opt/quast-5.0.2/quast_libs/qutils.py", line 180, in correct_contigs
old_fpaths, corr_fpaths, broken_scaffold_fpaths, logs, is_fatal_error = run_parallel(parallel_correct_contigs, parallel_run_args, n_jobs)
File "/shared/ifbstor1/software/miniconda/envs/quast-5.0.2/opt/quast-5.0.2/quast_libs/qutils.py", line 1064, in run_parallel
from joblib3 import Parallel, delayed
ModuleNotFoundError: No module named 'joblib3'
ERROR! exception caught!
Si je source un script pour charger plusieurs modules et préparer l'environment, j'ai l'erreur et quast ne fonctionne pas
Si je charge le module à la main, il n'y a pas d'erreur et quast fonctionne
voici la boucle utilisée pour le chrgement des modules (j'ai mis ça en place car je débute avec module et ne le connais pas assez pour lui faire charger une liste de modules préselectionnés).
for i in cat /shared/projects/form_2022_016/softwares/modules.list
do
MODULE=echo $i | cut -f 1 -d "/"
PRESENT=module list | grep -c ${MODULE}
if [[ "${PRESENT}" -eq "0" ]]
then
echo "loading module" $i
module load $i
fi
done
On peut aussi load plusieurs modules via un seul module load tool1/version tool2/version
Sinon, il faut toujours un peu se méfier quand on empile des modules. Par exemple, si plusieurs outils sont sur base de R, perl ou python, c'est le dernier module chargé qui gagne.
Ainsi, il est préférable de charger le module nécessaire juste avant de lancer l'outil :
mais indique des erreurs dans certains modules python, j'ai pu charger certains d'entre eux mais celui-ci n'a pas de solution :
module 'cgi' has no attribute 'escape'
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/quast-5.0.2/bin/quast", line 307, in
return_code = main(sys.argv[1:])
File "/shared/ifbstor1/software/miniconda/envs/quast-5.0.2/bin/quast", line 148, in main
from quast_libs import basic_stats
File "/shared/ifbstor1/software/miniconda/envs/quast-5.0.2/opt/quast-5.0.2/quast_libs/basic_stats.py", line 15, in
from quast_libs.circos import set_window_size
File "/shared/ifbstor1/software/miniconda/envs/quast-5.0.2/opt/quast-5.0.2/quast_libs/circos.py", line 25, in
from quast_libs.icarus_utils import get_assemblies, check_misassembled_blocks, Alignment
File "/shared/ifbstor1/software/miniconda/envs/quast-5.0.2/opt/quast-5.0.2/quast_libs/icarus_utils.py", line 15, in
from quast_libs.html_saver.html_saver import trim_ref_name
File "/shared/ifbstor1/software/miniconda/envs/quast-5.0.2/opt/quast-5.0.2/quast_libs/html_saver/html_saver.py", line 18, in
from quast_libs.site_packages.jsontemplate import jsontemplate
File "/shared/ifbstor1/software/miniconda/envs/quast-5.0.2/opt/quast-5.0.2/quast_libs/site_packages/jsontemplate/jsontemplate.py", line 583, in
'html': cgi.escape,
^^^^^^^^^^
AttributeError: module 'cgi' has no attribute 'escape'
ERROR! exception caught!
