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dohlee / chromoformer

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
GNU General Public License v3.0
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Error when running data processing snakemake script #9

Closed Al-Murphy closed 10 months ago

Al-Murphy commented 10 months ago

Hey,

I'm having issues running the snakemake script to download and process the data for Chromoformer. The command I'm using is:

snakemake --resources network=1 -j 32 --restart-times 3 --use-conda --conda-frontend mamba -pr

After installing snakemake via mamba following these steps.

The error I'm getting is:

CreateCondaEnvironmentException:
Could not create conda environment from /home/aemurphy/RDS/project/neurogenomics-lab/live/Projects/epi_to_express/chromoformer/preprocessing/environment.yaml:
Command:
mamba env create --quiet --file "/home/aemurphy/RDS/project/neurogenomics-lab/live/Projects/epi_to_express/chromoformer/preprocessing/.snakemake/conda/625986fa5c4238fed2ed240b2df7c3af_.yaml" --prefix "/home/aemurphy/RDS/project/neurogenomics-lab/live/Projects/epi_to_express/chromoformer/preprocessing/.snakemake/conda/625986fa5c4238fed2ed240b2df7c3af_"
....
[Errno 95] Operation not supported: 'cacert.pem' -> '/home/aemurphy/RDS/project/neurogenomics-lab/live/Projects/epi_to_express/chromoformer/preprocessing/.snakemake/conda/625986fa5c4238fed2ed240b2df7c3af_/ssl/cert.pem'
()

Full output is as follows:

(base) aemurphy@workstation:chromoformer/preprocessing$ snakemake --resources network=1 -j 32 --restart-times 3 --use-conda --conda-frontend mamba -pr Building DAG of jobs... Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'. Creating conda environment environment.yaml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create conda environment from /home/aemurphy/RDS/project/neurogenomics-lab/live/Projects/epi_to_express/chromoformer/preprocessing/environment.yaml: Command: mamba env create --quiet --file "/home/aemurphy/RDS/project/neurogenomics-lab/live/Projects/epi_to_express/chromoformer/preprocessing/.snakemake/conda/625986fa5c4238fed2ed240b2df7c3af_.yaml" --prefix "/home/aemurphy/RDS/project/neurogenomics-lab/live/Projects/epi_to_express/chromoformer/preprocessing/.snakemake/conda/625986fa5c4238fed2ed240b2df7c3af_" Output: Package Version Build Channel Size ─────────────────────────────────────────────────────────────────────────────────────────── Install: ─────────────────────────────────────────────────────────────────────────────────────────── + _libgcc_mutex 0.1 conda_forge conda-forge/linux-64 Cached + _openmp_mutex 4.5 2_gnu conda-forge/linux-64 Cached + bedtools 2.31.1 hf5e1c6e_0 bioconda/linux-64 Cached + bzip2 1.0.8 hd590300_5 conda-forge/linux-64 Cached + ca-certificates 2023.11.17 hbcca054_0 conda-forge/linux-64 Cached + colorama 0.4.6 pyhd8ed1ab_0 conda-forge/noarch Cached + ld_impl_linux-64 2.40 h41732ed_0 conda-forge/linux-64 Cached + ldc 1.28.1 hcf88599_0 conda-forge/linux-64 Cached + libblas 3.9.0 20_linux64_openblas conda-forge/linux-64 Cached + libcblas 3.9.0 20_linux64_openblas conda-forge/linux-64 Cached + libedit 3.1.20191231 he28a2e2_2 conda-forge/linux-64 Cached + libffi 3.4.2 h7f98852_5 conda-forge/linux-64 Cached + libgcc-ng 13.2.0 h807b86a_3 conda-forge/linux-64 Cached + libgfortran-ng 13.2.0 h69a702a_3 conda-forge/linux-64 Cached + libgfortran5 13.2.0 ha4646dd_3 conda-forge/linux-64 Cached + libgomp 13.2.0 h807b86a_3 conda-forge/linux-64 Cached + liblapack 3.9.0 20_linux64_openblas conda-forge/linux-64 Cached + libllvm12 12.0.1 hf817b99_2 conda-forge/linux-64 Cached + libnsl 2.0.1 hd590300_0 conda-forge/linux-64 Cached + libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge/linux-64 Cached + libsqlite 3.44.2 h2797004_0 conda-forge/linux-64 Cached + libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge/linux-64 Cached + libzlib 1.2.13 hd590300_5 conda-forge/linux-64 Cached + lz4-c 1.9.4 hcb278e6_0 conda-forge/linux-64 Cached + ncurses 6.4 h59595ed_2 conda-forge/linux-64 Cached + numpy 1.21.6 py37h976b520_0 conda-forge/linux-64 Cached + openssl 3.2.0 hd590300_1 conda-forge/linux-64 Cached + pandas 1.3.5 py37he8f5f7f_0 conda-forge/linux-64 Cached + pip 23.3.2 pyhd8ed1ab_0 conda-forge/noarch Cached + python 3.7.12 hf930737_100_cpython conda-forge/linux-64 Cached + python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge/noarch Cached + python_abi 3.7 4_cp37m conda-forge/linux-64 Cached + pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge/noarch Cached + readline 8.2 h8228510_1 conda-forge/linux-64 Cached + sambamba 1.0 h98b6b92_0 bioconda/linux-64 Cached + setuptools 59.8.0 py37h89c1867_1 conda-forge/linux-64 Cached + six 1.16.0 pyh6c4a22f_0 conda-forge/noarch Cached + sqlite 3.44.2 h2c6b66d_0 conda-forge/linux-64 Cached + tk 8.6.13 noxft_h4845f30_101 conda-forge/linux-64 Cached + tqdm 4.66.1 pyhd8ed1ab_0 conda-forge/noarch Cached + wheel 0.42.0 pyhd8ed1ab_0 conda-forge/noarch Cached + xz 5.2.6 h166bdaf_0 conda-forge/linux-64 Cached + zlib 1.2.13 hd590300_5 conda-forge/linux-64 Cached Summary: Install: 43 packages Total download: 0 B ─────────────────────────────────────────────────────────────────────────────────────────── Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done ERROR conda.core.link:_execute(945): An error occurred while installing package 'conda-forge::ca-certificates-2023.11.17-hbcca054_0'. Rolling back transaction: ...working... done [Errno 95] Operation not supported: 'cacert.pem' -> '/home/aemurphy/RDS/project/neurogenomics-lab/live/Projects/epi_to_express/chromoformer/preprocessing/.snakemake/conda/625986fa5c4238fed2ed240b2df7c3af_/ssl/cert.pem' ()

My snakemake version is 7.18.2. Any ideas on what could be going on here? Or anywhere to possibly download the data for the training scripts?

Thanks, Alan.

Al-Murphy commented 10 months ago

Just to also note, I tried creating the conda env in chromoformer/preprocessing/environment.yaml manually which worked but I got the same error when I reran the command

Al-Murphy commented 10 months ago

I got around the issue by just by passing snakemake and running the commands in ./preprocessing/Snakefile with the conda env in preprocessing/environment.yaml