Bonjour @gildaslecorguille,
je rentre de congés et essaye donc d'essayer mon outil tant attendu ... ça a l'air d'un mauvais scetch je suis désolée mais il crash toujours ...
voici la sortie d'erreur
Step : circlator
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/circlator", line 58, in
exec('circlator.tasks.' + task + '.run()')
File "", line 1, in
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/tasks/all.py", line 74, in run
circlator.versions.get_all_versions(None, raise_error=True, assembler=options.assembler)
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/versions.py", line 15, in get_all_versions
external_progs.check_all_progs(verbose=False, raise_error=raise_error, filehandle=filehandle, debug=debug, assembler=assembler)
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/external_progs.py", line 105, in check_all_progs
make_and_check_prog(prog, verbose=verbose, raise_error=raise_error, filehandle=filehandle, debug=debug, required=prog==assembler)
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/external_progs.py", line 78, in make_and_check_prog
handle_error('Found ' + name + " but couldn't get version.", raise_error=raise_error)
File "/shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/circlator/external_progs.py", line 53, in handle_error
raise Error(message + '\nCannot continue')
circlator.external_progs.Error: Found canu but couldn't get version.
Cannot continue
srun: error: cpu-node-19: task 0: Exited with exit code 1
Mbv-L15762C1 ok
Step 3 : circlator done
et la sortie de progcheck :
Circlator version: 1.5.5
External dependencies:
bwa 0.7.17 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/bwa
Found canu but couldn't get version.
nucmer 3.1 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/nucmer
prodigal 2.6.3 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/prodigal
Found samtools but couldn't get version.
spades 3.13.0 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/bin/spades.py
Python version:
3.6.12 | packaged by conda-forge | (default, Dec 9 2020, 00:36:02)
[GCC 9.3.0]
Python dependencies:
openpyxl 3.0.6 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/openpyxl/init.py
pyfastaq 3.17.0 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/pyfastaq/init.py
pymummer 0.11.0 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/pymummer/init.py
pysam 0.15.3 /shared/ifbstor1/software/miniconda/envs/circlator-1.5.5/lib/python3.6/site-packages/pysam/init.py
WARNING: SPAdes version 3.13.0 is being used. It will work, but better results are usually obtained from Circlator using SPAdes version 3.7.1. Although 3.7.1 is not the latest version, we recommend it for Circlator.
encore toutes mes excuses, c'est super frustrant des 2 côtés mais un grand merci d'avance
Chloé