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genomicsITER / NanoCLUST

NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
MIT License
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Failed to create Conda environment #39

Open timregan opened 3 years ago

timregan commented 3 years ago

Hi there,

I haven't been able to complete a successful run. It seems to have an issue creating a conda environment (conda otherwise seems to be working perfectly).

Output as follows:

` NanoCLUST v1.0dev

Run Name : amazing_jepsen Reads : Larvae_waste.fastq Max Resources : 128 GB memory, 16 cpus, 10d time per job Output dir : ./results Launch dir : /exports/eddie/scratch/tregan/NanoCLUST Working dir : /exports/eddie/scratch/tregan/NanoCLUST/work Script dir : /exports/eddie/scratch/tregan/NanoCLUST User : tregan Config Profile : conda

executor > local (1) [7f/4a6a0e] process > QC (1) [100%] 1 of 1 ✔ [- ] process > fastqc - [- ] process > kmer_freqs - [- ] process > read_clustering - [- ] process > split_by_cluster - [- ] process > read_correction - [- ] process > draft_selection - [- ] process > racon_pass - [- ] process > medaka_pass - [- ] process > consensus_classification - [- ] process > join_results - [- ] process > get_abundances - [- ] process > plot_abundances - [- ] process > output_documentation - Creating Conda env: /exports/eddie/scratch/tregan/NanoCLUST/conda_envs/kmer_freqs/environment.yml [cache /exports/eddie/scratch/tregan/NanoCLUST/work/conda/kmer_freq-999fbd7473cd6106e662a85d832c592d] executor > local (1) executor > local (1) [7f/4a6a0e] process > QC (1) [100%] 1 of 1 ✔ [- ] process > fastqc - [- ] process > kmer_freqs - [- ] process > read_clustering - [- ] process > split_by_cluster - [- ] process > read_correction - [- ] process > draft_selection - [- ] process > racon_pass - [- ] process > medaka_pass - [- ] process > consensus_classification - [- ] process > join_results - [- ] process > get_abundances - [- ] process > plot_abundances - [- ] process > output_documentation - Error executing process > 'output_documentation'

Caused by: Failed to create Conda environment command: conda env create --prefix /exports/eddie/scratch/tregan/NanoCLUST/work/conda/output-documentation-f87367ab9ec78f3fc18fcdbf466b1827 --file /exports/eddie/scratch/tregan/NanoCLUST/conda_envs/output_documentation/environment.yml status : 143 message: `

Many thanks, Tim

genomicsITER commented 3 years ago

Hi,

We've got similar errors while testing the pipeline environments. I would recommend to clean all directories that may have been created as output (work, results). Some problems could arise if you have multiple versions of dependencies. A conda clean command have solved 143 errors for us.

Alternatively, the pipeline can use Docker containers to build the computing environments.