Installation log

gistfile1.txt

The flag 'directory' used in rule awk_parsing_alignment is only valid for outputs, not inputs.
Building DAG of jobs...
Creating conda environment envs/r_packages.yaml...
Downloading remote packages.
Environment for envs/r_packages.yaml created (location: .snakemake/conda/8b80b155)
Using shell: /bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	awk_links
	1	awk_nodes
	1	gplas_coocurr
	1	gplas_coverage
	1	gplas_paths
	1	mlplasmids
	6

[Thu Sep 12 16:02:26 2019]
Job 1: Extracting the nodes from the graph test/faecium_graph.gfa

Activating conda environment: /home/ubuntu/Legionella10T/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/8b80b155
[Thu Sep 12 16:02:32 2019]
Finished job 1.
1 of 6 steps (17%) done

[Thu Sep 12 16:02:32 2019]
Job 5: Extracting the links from the graph test/faecium_graph.gfa

Activating conda environment: /home/ubuntu/Legionella10T/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/8b80b155
[Thu Sep 12 16:02:38 2019]
Finished job 5.
2 of 6 steps (33%) done

[Thu Sep 12 16:02:38 2019]
Job 3: Running mlplasmids to obtain the plasmid prediction using the nodes extracted from the graph. If this is the first time running mlplasmids, installation can take a few minutes

Activating conda environment: /home/ubuntu/Legionella10T/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/8b80b155
[Thu Sep 12 16:07:33 2019]
Finished job 3.
3 of 6 steps (50%) done

[Thu Sep 12 16:07:33 2019]
Job 2: Extracting the sd k-mer coverage from the chromosome-predicted contigs

Activating conda environment: /home/ubuntu/Legionella10T/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/8b80b155
[Thu Sep 12 16:07:49 2019]
Finished job 2.
4 of 6 steps (67%) done

[Thu Sep 12 16:07:49 2019]
Job 4: Searching for plasmid-like paths using a greedy approach

Activating conda environment: /home/ubuntu/Legionella10T/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/8b80b155
[Thu Sep 12 16:08:37 2019]
Finished job 4.
5 of 6 steps (83%) done

[Thu Sep 12 16:08:37 2019]
Job 0: Creating a co-occurrence network and selecting significant associations between nodes.

Activating conda environment: /home/ubuntu/Legionella10T/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/8b80b155
[Thu Sep 12 16:09:42 2019]
Finished job 0.
6 of 6 steps (100%) done
Complete log: /home/ubuntu/Legionella10T/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/log/2019-09-12T160053.343430.snakemake.log