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Error during running: Error in rule gplas_paths

./gplas.sh -i /data/nihr/ghru_retrospective_R1_R2/center_wise_data/RDG/full_assembly_out/spades_out/G18254647/assembly_graph_after_simplification.gfa -c 'mlplasmids' -s 'Escherichia coli'



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


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This is your input graph: /data/nihr/ghru_retrospective_R1_R2/center_wise_data/RDG/full_assembly_out/spades_out/G18254647/assembly_graph_after_simplification.gfa 

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

You did not pass an output name. Your results will be named as 'unnamed' 

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 walks based on each plasmid seed, using 20 as default

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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: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	gplas_coocurr
	1	gplas_paths
	2

[Mon Jun  6 12:37:49 2022]
Job 4: Searching for plasmid-like walks using a greedy approach

Activating conda environment: /data/nihr/nanopore_sequencing/KPN/2022-02-02/hybrid_assembly_output/gplas/.snakemake/conda/dabd0ead
Error in `$<-.data.frame`(`*tmp*`, number, value = character(0)) : 
  replacement has 0 rows, data has 1
Calls: $<- -> $<-.data.frame
Execution halted
[Mon Jun  6 12:37:53 2022]
Error in rule gplas_paths:
    jobid: 4
    output: walks/unnamed_solutions.csv, walks/unnamed_connections.tab
    conda-env: /data/nihr/nanopore_sequencing/KPN/2022-02-02/hybrid_assembly_output/gplas/.snakemake/conda/dabd0ead

RuleException:
CalledProcessError in line 97 of /data/nihr/nanopore_sequencing/KPN/2022-02-02/hybrid_assembly_output/gplas/mlplasmidssnake.smk:
Command 'source /home/anaconda/miniconda3/bin/activate '/data/nihr/nanopore_sequencing/KPN/2022-02-02/hybrid_assembly_output/gplas/.snakemake/conda/dabd0ead'; set -euo pipefail;  Rscript --vanilla /data/nihr/nanopore_sequencing/KPN/2022-02-02/hybrid_assembly_output/gplas/.snakemake/scripts/tmpua35fmjc.gplas_paths.R' returned non-zero exit status 1.
  File "/data/nihr/nanopore_sequencing/KPN/2022-02-02/hybrid_assembly_output/gplas/mlplasmidssnake.smk", line 97, in __rule_gplas_paths
  File "/home/varuns/.conda/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: /data/nihr/nanopore_sequencing/KPN/2022-02-02/hybrid_assembly_output/gplas/.snakemake/log/2022-06-06T123749.486555.snakemake.log
Looks like something went wrong!

Installation works fine.

I tried running gplas on both spades .gfa and unicycler .gfa I get the same error for both. i couldn't figure out why this is happening. If you want I will send my assembly graphs also.