Conda probleme build

IFB Core Cluster
1

Bonjour,
j'ai des problèmes pour builder des environnement conda, avez vous une idée? j'ai des erreurs de ce type. ça marchait il y a deux semaines :sweat_smile:

Merci!!

Creating conda environment /shared/ifbstor1/home/jorjuela/softs/CulebrONT_pipeline/envs/nanopolish_minimap2_samtools_seqtk.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /shared/ifbstor1/home/jorjuela/softs/CulebrONT_pipeline/envs/nanopolish_minimap2_samtools_seqtk.yaml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working...
Building graph of deps: 0%| | 0/8 [00:00<?, ?it/s]
Examining minimap2=2.17: 0%| | 0/8 [00:00<?, ?it/s]
Examining seqtk=1.3: 12%|█▎ | 1/8 [00:00<00:00, 138.72it/s]
Examining @/linux-64::__archspec==1=x86_64: 25%|██▌ | 2/8 [00:00<00:00, 149.47it/s]
Examining samtools=1.10: 38%|███▊ | 3/8 [00:00<00:00, 220.81it/s]
Examining python=3.7: 50%|█████ | 4/8 [00:00<00:00, 169.27it/s]
Examining nanopolish=0.13.2: 62%|██████▎ | 5/8 [00:01<00:00, 3.16it/s]
Examining nanopolish=0.13.2: 75%|███████▌ | 6/8 [00:01<00:00, 3.79it/s]
Examining @/linux-64::__unix==0=0: 75%|███████▌ | 6/8 [00:01<00:00, 3.79it/s]
Examining @/linux-64::__unix==0=0: 88%|████████▊ | 7/8 [00:01<00:00, 3.56it/s]
Examining @/linux-64::__glibc==2.17=0: 88%|████████▊ | 7/8 [00:01<00:00, 3.56it/s]

Determining conflicts: 0%| | 0/8 [00:00<?, ?it/s]
Examining conflict for minimap2 nanopolish: 0%| | 0/8 [00:00<?, ?it/s]
Examining conflict for minimap2 seqtk samtools python nanopolish: 12%|█▎ | 1/8 [00:00<00:00, 1519.12it/s]
Examining conflict for minimap2 python nanopolish samtools: 25%|██▌ | 2/8 [00:00<00:00, 23.82it/s]
Examining conflict for python nanopolish samtools: 38%|███▊ | 3/8 [00:00<00:00, 13.63it/s]
Examining conflict for python nanopolish samtools: 50%|█████ | 4/8 [00:00<00:00, 18.16it/s]
Examining conflict for nanopolish samtools: 50%|█████ | 4/8 [00:00<00:00, 18.16it/s]
Examining conflict for nanopolish samtools: 62%|██████▎ | 5/8 [00:00<00:00, 7.78it/s]
Examining conflict for python nanopolish: 62%|██████▎ | 5/8 [00:00<00:00, 7.78it/s]
Examining conflict for python nanopolish: 75%|███████▌ | 6/8 [00:00<00:00, 5.33it/s]

Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
Solving environment: ...working...

Building graph of deps: 0%| | 0/8 [00:00<?, ?it/s]
Examining minimap2=2.17: 0%| | 0/8 [00:00<?, ?it/s]
Examining seqtk=1.3: 12%|█▎ | 1/8 [00:00<00:00, 127.75it/s]
Examining @/linux-64::__archspec==1=x86_64: 25%|██▌ | 2/8 [00:00<00:00, 151.58it/s]
Examining samtools=1.10: 38%|███▊ | 3/8 [00:00<00:00, 223.82it/s]
Examining python=3.7: 50%|█████ | 4/8 [00:00<00:00, 168.17it/s]
Examining nanopolish=0.13.2: 62%|██████▎ | 5/8 [00:01<00:00, 3.26it/s]
Examining nanopolish=0.13.2: 75%|███████▌ | 6/8 [00:01<00:00, 3.91it/s]
Examining @/linux-64::__unix==0=0: 75%|███████▌ | 6/8 [00:01<00:00, 3.91it/s]
Examining @/linux-64::__unix==0=0: 88%|████████▊ | 7/8 [00:01<00:00, 3.59it/s]
Examining @/linux-64::__glibc==2.17=0: 88%|████████▊ | 7/8 [00:01<00:00, 3.59it/s]

Determining conflicts: 0%| | 0/8 [00:00<?, ?it/s]
Examining conflict for minimap2 nanopolish: 0%| | 0/8 [00:00<?, ?it/s]
Examining conflict for minimap2 seqtk samtools python nanopolish: 12%|█▎ | 1/8 [00:00<00:00, 1596.61it/s]
Examining conflict for minimap2 python nanopolish samtools: 25%|██▌ | 2/8 [00:00<00:00, 22.73it/s]
Examining conflict for python nanopolish samtools: 38%|███▊ | 3/8 [00:00<00:00, 13.01it/s]
Examining conflict for python nanopolish samtools: 50%|█████ | 4/8 [00:00<00:00, 17.34it/s]
Examining conflict for nanopolish samtools: 50%|█████ | 4/8 [00:00<00:00, 17.34it/s]
Examining conflict for nanopolish samtools: 62%|██████▎ | 5/8 [00:00<00:00, 7.53it/s]
Examining conflict for python nanopolish: 62%|██████▎ | 5/8 [00:00<00:00, 7.53it/s]
Examining conflict for python nanopolish: 75%|███████▌ | 6/8 [00:00<00:00, 5.14it/s]

Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libgcc-ng conflicts for:
minimap2=2.17 -> libgcc-ng[version='>=7.3.0|>=7.5.0']
minimap2=2.17 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='7.2.0.*|>=4.9|>=7.2.0']

Package libstdcxx-ng conflicts for:
nanopolish=0.13.2 -> biopython -> libstdcxx-ng[version='7.2.0.*|>=4.9|>=7.2.0|>=9.3.0']
python=3.7 -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=7.2.0']
samtools=1.10 -> ncurses[version='>=6.2,<6.3.0a0'] -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=7.2.0']
minimap2=2.17 -> libstdcxx-ng[version='>=7.3.0']
minimap2=2.17 -> k8 -> libstdcxx-ng[version='>=7.5.0']
python=3.7 -> libffi[version='>=3.2.1,<3.3.0a0'] -> libstdcxx-ng=7.2.0
nanopolish=0.13.2 -> libstdcxx-ng[version='>=7.3.0|>=7.5.0']

Package zlib conflicts for:
seqtk=1.3 -> zlib[version='>=1.2.11,<1.3.0a0']
samtools=1.10 -> zlib[version='>=1.2.11,<1.3.0a0']
nanopolish=0.13.2 -> zlib[version='>=1.2.11,<1.3.0a0']
minimap2=2.17 -> zlib[version='>=1.2.11,<1.3.0a0']
python=3.7 -> zlib[version='>=1.2.11,<1.3.0a0']
nanopolish=0.13.2 -> bwa -> zlib[version='1.2.|1.2.11|1.2.11.|1.2.8.*|1.2.8']

Package minimap2 conflicts for:
minimap2=2.17
nanopolish=0.13.2 -> minimap2

Package libcurl conflicts for:
samtools=1.10 -> htslib[version='>=1.10.2,<1.11.0a0'] -> libcurl[version='>=7.64.1,<8.0a0|>=7.71.1,<8.0a0']
nanopolish=0.13.2 -> libcurl[version='>=7.64.1,<8.0a0|>=7.69.1,<8.0a0|>=7.71.1,<8.0a0']

Package python conflicts for:
python=3.7
nanopolish=0.13.2 -> python
nanopolish=0.13.2 -> biopython -> python[version='2.7.|3.5.|3.6.|3.4.|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']

Package xz conflicts for:
python=3.7 -> xz[version='>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0']
nanopolish=0.13.2 -> htslib[version='>=1.10.2,<1.11.0a0'] -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
samtools=1.10 -> htslib[version='>=1.10.2,<1.11.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']

Package ncurses conflicts for:
python=3.7 -> readline[version='>=7.0,<8.0a0'] -> ncurses[version='5.9.|>=6.0,<7.0a0|6.0.']
python=3.7 -> ncurses[version='>=6.1,<6.3.0a0|>=6.2,<6.3.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0']

Package libdeflate conflicts for:
nanopolish=0.13.2 -> htslib[version='>=1.10.2,<1.11.0a0'] -> libdeflate[version='>=1.0,<1.1.0a0|>=1.3,<1.4.0a0|>=1.6,<1.7.0a0']
nanopolish=0.13.2 -> libdeflate
Note that strict channel priority may have removed packages required for satisfiability.

File "/shared/home/jorjuela/.local/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 350, in create

2

Bonjour,

Pour nous permettre d'analyser le souci, pouvez partager votre fichier env.yml qui sert a créer l’environnement conda ?

Vous pouvez aussi essayer avec mamba qui est installé au même endroit que conda. Il suffit de remplacer le binaire "conda" par "mamba" dans vos scripts.
Peut-être que mamba sans sortira mieux, et si c'est pas la cas, alors au moins le message d'erreur remonté par mamba sera + explicite que celui de conda.

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4

Bonjour à tous,
Belle année :slight_smile:
en fait le build se fait à travers snakemake,
en effet lors que je lance mamba env create -f nanopolish_minimap2_samtools_seqtk.yaml l'env se build bien comme il faut.
J'ai vu qu'il y a un paramètre snakemake --conda-frontend pour choisir conda ou mamba, j'ai donc buildé depuis la commande snake en utilisant ce paramettre avec mamba et ça à l'air de marcher ...
pour info les yaml sont dans /shared/ifbstor1/home/jorjuela/softs/CulebrONT_pipeline/envs/*.yaml
Merci bcp pour la piste :nerd_face:

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