gistfile1.txt

bash-4.1$ ./gplas.sh -i /disk2/bwee/projects/ecoli/starcs/anl/gplas/run1_test_UZ/102991-003-253_spades/assembly_graph_with_scaffolds.gfa -c mlplasmids -s 'Escherichia coli' -n '102991-003-253'


  _______ .______    __           ___           _______.
 /  _____||   _  \  |  |         /   \         /       |
|  |  __  |  |_)  | |  |        /  ^  \       |   (----`
|  | |_ | |   ___/  |  |       /  /_\  \       \   \
|  |__| | |  |      |  `----. /  _____  \  .----)   |
 \______| | _|      |_______|/__/     \__\ |_______/


##################################################################


This is your input graph: /disk2/bwee/projects/ecoli/starcs/anl/gplas/run1_test_UZ/102991-003-253_spades/assembly_graph_with_scaffolds.gfa

This is the bacterial species that you have indicated: Escherichia coli

Your results will be named  102991-003-253

You did not indicate a threshold prediction. Using 0.5 because you are using mlplasmids

You did not pass the number of times to look for paths based on each plasmid seed, using 20 as default

##################################################################
Conda is present

Creating (only the first-time) a conda environment to install and run snakemake
The flag 'directory' used in rule awk_parsing_alignment is only valid for outputs, not inputs.
Building DAG of jobs...
Unlocking working directory.
The flag 'directory' used in rule awk_parsing_alignment is only valid for outputs, not inputs.
Building DAG of jobs...
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 17:11:52 2019]
Job 5: Extracting the links from the graph /disk2/bwee/projects/ecoli/starcs/anl/gplas/run1_test_UZ/102991-003-253_spades/assembly_graph_with_scaffolds.gfa

Activating conda environment: /disk2/bwee/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/ea45a578
[Thu Sep 12 17:11:57 2019]
Finished job 5.
1 of 6 steps (17%) done

[Thu Sep 12 17:11:57 2019]
Job 1: Extracting the nodes from the graph /disk2/bwee/projects/ecoli/starcs/anl/gplas/run1_test_UZ/102991-003-253_spades/assembly_graph_with_scaffolds.gfa

Activating conda environment: /disk2/bwee/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/ea45a578
[Thu Sep 12 17:12:00 2019]
Finished job 1.
2 of 6 steps (33%) done

[Thu Sep 12 17:12:00 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: /disk2/bwee/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/ea45a578
[Thu Sep 12 17:12:11 2019]
Finished job 3.
3 of 6 steps (50%) done

[Thu Sep 12 17:12:11 2019]
Job 2: Extracting the sd k-mer coverage from the chromosome-predicted contigs

Activating conda environment: /disk2/bwee/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/ea45a578
Warning message:
NAs introduced by coercion
[Thu Sep 12 17:12:38 2019]
Finished job 2.
4 of 6 steps (67%) done

[Thu Sep 12 17:12:38 2019]
Job 4: Searching for plasmid-like paths using a greedy approach

Activating conda environment: /disk2/bwee/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/ea45a578
[Thu Sep 12 17:13:21 2019]
Finished job 4.
5 of 6 steps (83%) done

[Thu Sep 12 17:13:21 2019]
Job 0: Creating a co-occurrence network and selecting significant associations between nodes.

Activating conda environment: /disk2/bwee/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/ea45a578
Error in 1:nrow(no_duplicated) : argument of length 0
Execution halted
[Thu Sep 12 17:13:57 2019]
Error in rule gplas_coocurr:
    jobid: 0
    output: results/102991-003-253_plasmidome_network.png, results/102991-003-253_components.tab, results/102991-003-253_results.tab
    conda-env: /disk2/bwee/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/ea45a578

RuleException:
CalledProcessError in line 124 of /disk2/bwee/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/mlplasmidssnake.smk:
Command 'source /localdisk/home/bwee/miniconda3/bin/activate '/disk2/bwee/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/ea45a578'; set -euo pipefail;  Rscript --vanilla /disk2/bwee/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/scripts/tmpsx34cjix.gplas_coocurrence.R' returned non-zero exit status 1.
  File "/disk2/bwee/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/mlplasmidssnake.smk", line 124, in __rule_gplas_coocurr
  File "/localdisk/home/bwee/miniconda3/envs/gplas/lib/python3.7/concurrent/futures/thread.py", line 57, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /disk2/bwee/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/log/2019-09-12T171152.745192.snakemake.log
Looks like something went wrong!