Invalid index Error, but model runs fine on GUI

[pdh21]

I am trying to run my model using Circuitscape.jl but run into the following error:

[ Info: 2022-11-08 13:55:36 : Logs will recorded to file: log_file
[ Info: 2022-11-08 13:55:36 : Precision used: Double
┌ Info: 2022-11-08 13:55:36 : Circuitscape.jl starts counting nodes from 1,
└ not 0. This will be reflected in the outputs.
[ Info: 2022-11-08 13:55:36 : Time taken to construct graph laplacian = 4.5e-6 
[ Info: 2022-11-08 13:55:36 : Solver used: AMG accelerated by CG 
[ Info: 2022-11-08 13:55:36 : Graph has 11 nodes, 11 focal points and 1 connected components 
[ Info: 2022-11-08 13:55:36 : Total number of pair solves = 55                                                          
[ Info: 2022-11-08 13:55:36 : Time taken to construct preconditioner = 5.74e-5 seconds                                  
[ Info: 2022-11-08 13:55:36 : Time taken to construct local nodemap = 1.7e-6 seconds                                    
[ Info: 2022-11-08 13:55:36 : Solving pair 1 of 55                                                                      
[ Info: 2022-11-08 13:55:36 : Time taken to solve linear system = 1.61e-5 seconds                                       
[ Info: 2022-11-08 13:55:36 : Time taken to write voltage maps = 0.0007811 seconds                                      
ERROR: ArgumentError: invalid index: nothing of type Nothing                                                            
Stacktrace:                                                                                                               
[1] to_index(i::Nothing)                                                                                                  
@ Base .\indices.jl:300                                                                                               
[2] to_index(A::SharedArrays.SharedVector{Float64}, i::Nothing)                                                           
@ Base .\indices.jl:277                                                                                               
[3] to_indices                                                                                                            
@ .\indices.jl:333 [inlined]                                                                                          
[4] to_indices                                                                                                            
@ .\indices.jl:325 [inlined]                                                                                          
[5] getindex                                                                                                              
@ .\abstractarray.jl:1241 [inlined]                                                                                   
[6] write_cur_maps(name::String, output::Circuitscape.Output{Float64, Int64}, component_data::Circuitscape.ComponentData{Float64, Int64}, finitegrounds::Vector{Float64}, flags::Circuitscape.NetworkFlags, cfg::Dict{String, String})            
@ Circuitscape C:\Users\hurleyp\.julia\packages\Circuitscape\XpftG\src\out.jl:73                                      
[7] macro expansion                                                                                                       
@ .\timing.jl:382 [inlined]                                                                                           
[8] postprocess(output::Circuitscape.Output{Float64, Int64}, component_data::Circuitscape.ComponentData{Float64, Int64}, flags::Circuitscape.NetworkFlags, shortcut::Circuitscape.Shortcut{Float64}, cfg::Dict{String, String})                   
@ Circuitscape C:\Users\hurleyp\.julia\packages\Circuitscape\XpftG\src\core.jl:667                                    
[9] (::Circuitscape.var"#f#100"{Float64, Int64, Circuitscape.NetworkFlags, Dict{String, String}, Bool, Circuitscape.Shortcut{Float64}, Circuitscape.Cumulative{Float64, Int64}, Vector{Int64}, Vector{Tuple{Int64, Int64}}, Vector{Int64}, Vector{Int64}, Circuitscape.ComponentData{Float64, Int64}, AlgebraicMultigrid.Preconditioner{AlgebraicMultigrid.MultiLevel{AlgebraicMultigrid.Pinv{Float64}, AlgebraicMultigrid.GaussSeidel{AlgebraicMultigrid.SymmetricSweep}, AlgebraicMultigrid.GaussSeidel{AlgebraicMultigrid.SymmetricSweep}, SparseArrays.SparseMatrixCSC{Float64, Int64}, SparseArrays.SparseMatrixCSC{Float64, Int64}, LinearAlgebra.Adjoint{Float64, SparseArrays.SparseMatrixCSC{Float64, Int64}}, AlgebraicMultigrid.MultiLevelWorkspace{Vector{Float64}, 1}}, AlgebraicMultigrid.V}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Int64}})(i::Int64)                                                                                                               
@ Circuitscape C:\Users\hurleyp\.julia\packages\Circuitscape\XpftG\src\core.jl:231                                   
[10] #98                                                                                                                   
@ C:\Users\hurleyp\.julia\packages\Circuitscape\XpftG\src\core.jl:251 [inlined]                                      
[11] iterate                                                                                                               
@ .\generator.jl:47 [inlined]                                                                                        
[12] _collect(c::UnitRange{Int64}, itr::Base.Generator{UnitRange{Int64}, Circuitscape.var"#98#104"{Circuitscape.var"#f#100"{Float64, Int64, Circuitscape.NetworkFlags, Dict{String, String}, Bool, Circuitscape.Shortcut{Float64}, Circuitscape.Cumulative{Float64, Int64}, Vector{Int64}, Vector{Tuple{Int64, Int64}}, Vector{Int64}, Vector{Int64}, Circuitscape.ComponentData{Float64, Int64}, AlgebraicMultigrid.Preconditioner{AlgebraicMultigrid.MultiLevel{AlgebraicMultigrid.Pinv{Float64}, AlgebraicMultigrid.GaussSeidel{AlgebraicMultigrid.SymmetricSweep}, AlgebraicMultigrid.GaussSeidel{AlgebraicMultigrid.SymmetricSweep}, SparseArrays.SparseMatrixCSC{Float64, Int64}, SparseArrays.SparseMatrixCSC{Float64, Int64}, LinearAlgebra.Adjoint{Float64, SparseArrays.SparseMatrixCSC{Float64, Int64}}, AlgebraicMultigrid.MultiLevelWorkspace{Vector{Float64}, 1}}, AlgebraicMultigrid.V}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Int64}}}}, #unused#::Base.EltypeUnknown, isz::Base.HasShape{1})                                     @ Base .\array.jl:807                                                                                                
[13] collect_similar(cont::UnitRange{Int64}, itr::Base.Generator{UnitRange{Int64}, Circuitscape.var"#98#104"{Circuitscape.var"#f#100"{Float64, Int64, Circuitscape.NetworkFlags, Dict{String, String}, Bool, Circuitscape.Shortcut{Float64}, Circuitscape.Cumulative{Float64, Int64}, Vector{Int64}, Vector{Tuple{Int64, Int64}}, Vector{Int64}, Vector{Int64}, Circuitscape.ComponentData{Float64, Int64}, AlgebraicMultigrid.Preconditioner{AlgebraicMultigrid.MultiLevel{AlgebraicMultigrid.Pinv{Float64}, AlgebraicMultigrid.GaussSeidel{AlgebraicMultigrid.SymmetricSweep}, AlgebraicMultigrid.GaussSeidel{AlgebraicMultigrid.SymmetricSweep}, SparseArrays.SparseMatrixCSC{Float64, Int64}, SparseArrays.SparseMatrixCSC{Float64, Int64}, LinearAlgebra.Adjoint{Float64, SparseArrays.SparseMatrixCSC{Float64, Int64}}, AlgebraicMultigrid.MultiLevelWorkspace{Vector{Float64}, 1}}, AlgebraicMultigrid.V}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Int64}}}})                  
@ Base .\array.jl:716                                         
[14] map(f::Function, A::UnitRange{Int64})                                                                                 
@ Base .\abstractarray.jl:2933                                                                                       
[15] solve(prob::Circuitscape.GraphProblem{Float64, Int64, Circuitscape.AMGSolver}, #unused#::Circuitscape.AMGSolver, flags::Circuitscape.NetworkFlags, cfg::Dict{String, String}, log::Bool)                                                      
@ Circuitscape C:\Users\hurleyp\.julia\packages\Circuitscape\XpftG\src\core.jl:251                                   
[16] single_ground_all_pairs (repeats 2 times)                                                                             
@ C:\Users\hurleyp\.julia\packages\Circuitscape\XpftG\src\core.jl:66 [inlined]                                       
[17] network_pairwise(T::Type, V::Type, cfg::Dict{String, String})                                                         
@ Circuitscape C:\Users\hurleyp\.julia\packages\Circuitscape\XpftG\src\network\pairwise.jl:16                        
[18] _compute(T::Type, V::Type, cfg::Dict{String, String})                                                                 
@ Circuitscape C:\Users\hurleyp\.julia\packages\Circuitscape\XpftG\src\run.jl:53                                     
[19] macro expansion                                                                                                       
@ .\timing.jl:382 [inlined]                                                                                          
[20] compute(path::String)                                                                                                 
@ Circuitscape C:\Users\hurleyp\.julia\packages\Circuitscape\XpftG\src\run.jl:31                                     
[21] top-level scope                                                                                                       
@ REPL[26]:1 

INI file

[Options for advanced mode]
ground_file_is_resistances = True
remove_src_or_gnd = keepall
ground_file = (Browse for a ground point file)
use_unit_currents = False
source_file = (Browse for a current source file)
use_direct_grounds = False

[Mask file]
mask_file = (Browse for a raster mask file)
use_mask = False

[Calculation options]
low_memory_mode = False
parallelize = False
solver = cg+amg
print_timings = 1
preemptive_memory_release = False
print_rusages = False
max_parallel = 0

[Short circuit regions (aka polygons)]
polygon_file = (Browse for a short-circuit region file)
use_polygons = False

[Options for one-to-all and all-to-one modes]
use_variable_source_strengths = False
variable_source_file = (Browse for a source strength file)

[Output options]
set_null_currents_to_nodata = False
set_focal_node_currents_to_zero = False
set_null_voltages_to_nodata = False
compress_grids = False
write_cur_maps = 1
write_volt_maps = 0
output_file = test_small_10.out
write_cum_cur_map_only = True
log_transform_maps = False
write_max_cur_maps = False

[Version]
version = 4.0.5

[Options for reclassification of habitat data]
reclass_file = (Browse for file with reclassification data)
use_reclass_table = False

[Logging Options]
log_level = INFO
log_file = test_small_10.log
profiler_log_file = test_small_10__rusages.log
screenprint_log = False

[Options for pairwise and one-to-all and all-to-one modes]
included_pairs_file = (Browse for a file with pairs to include or exclude)
use_included_pairs = False
point_file = input_focal_nodes_10.txt

[Connection scheme for raster habitat data]
connect_using_avg_resistances = False
connect_four_neighbors_only = False

[Habitat raster or graph]
habitat_map_is_resistances = True
habitat_file = input_resist_test_10.txt

[Circuitscape mode]
data_type = network
scenario = pairwise

resistance file

0.000000000000000e+00 2.000000000000000e+00 1.000000000000000e+01
0.000000000000000e+00 5.000000000000000e+00 1.000000000000000e+01
0.000000000000000e+00 8.000000000000000e+00 1.000000000000000e+01
0.000000000000000e+00 7.000000000000000e+00 1.000000000000000e+01
1.000000000000000e+00 7.000000000000000e+00 5.000000000000000e+00
1.000000000000000e+00 4.000000000000000e+00 5.000000000000000e+00
2.000000000000000e+00 4.000000000000000e+00 1.000000000000000e+00
2.000000000000000e+00 6.000000000000000e+00 1.000000000000000e+00
2.000000000000000e+00 7.000000000000000e+00 1.000000000000000e+00
2.000000000000000e+00 1.000000000000000e+01 1.000000000000000e+00
3.000000000000000e+00 9.000000000000000e+00 1.000000000000000e+01
3.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+01
3.000000000000000e+00 4.000000000000000e+00 1.000000000000000e+01
4.000000000000000e+00 6.000000000000000e+00 1.000000000000000e+00
4.000000000000000e+00 7.000000000000000e+00 1.000000000000000e+00
4.000000000000000e+00 9.000000000000000e+00 1.000000000000000e+00
5.000000000000000e+00 1.000000000000000e+01 1.000000000000000e+01
5.000000000000000e+00 2.000000000000000e+00 1.000000000000000e+01
6.000000000000000e+00 9.000000000000000e+00 1.000000000000000e+00
6.000000000000000e+00 1.000000000000000e+01 1.000000000000000e+00
8.000000000000000e+00 7.000000000000000e+00 1.000000000000000e+01

Focal node file

0.000000000000000e+00
1.000000000000000e+00
2.000000000000000e+00
3.000000000000000e+00
4.000000000000000e+00
5.000000000000000e+00
6.000000000000000e+00
7.000000000000000e+00
8.000000000000000e+00
9.000000000000000e+00
1.000000000000000e+01

Circuitscape and Julia version
Circuitscape v5.11.2 and Julia v1.8.1

Additional context
The same ini and input files work fine with the GUI. I have also tried two tests from Circuitscape\test\inputs, mgNetworkVerify3.ini and sgNetworkVerify1.ini . Both of these work without any issues. I am on Windows, but I have also tried running via docker and get the same issue.

Any guidance or help would be much appreciated. Thanks

[ranjanan]

Thanks, I'll take a look.