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intervene-EU-H2020 / synthetic_data

Software program for generating synthetic datasets for genotypes and phenotypes
GNU General Public License v3.0
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Error during genotype generation #30

Open bruno-ariano opened 9 months ago

bruno-ariano commented 9 months ago

Hi, I have got this error while running the geno process. This happened each time I sent the job on a different chromosome during the processing with the following error: Progress: 91%|█████████████████████████████████████▎ | ETA: 0:00:16ERROR: LoadError: Progress: 91%|█████████████████████████████████████▎ | ETA: 0:00:16TaskFailedException

Stacktrace: [1] wait @ ./task.jl:322 [inlined] [2] threading_run(func::Function) @ Base.Threads ./threadingconstructs.jl:34 [3] macro expansion @ ./threadingconstructs.jl:93 [inlined] [4] get_genostr(batch_ref_df::DataFrame, batchsize::Int64, start_haplotype::Int64, metadata::GenomicMetadata) @ Main /opt/intervene/scripts/algorithms/genotype/write_output.jl:60 [5] write_to_plink_batch(batch_ref_df::DataFrame, prev_batchsize::Int64, cur_batchsize::Int64, batch_number::Int64, metadata::GenomicMetadata) @ Main /opt/intervene/scripts/algorithms/genotype/write_output.jl:115 [6] create_synthetic_genotype_for_chromosome(metadata::GenomicMetadata) @ Main /opt/intervene/scripts/algorithms/genotype/genotype_algorithm.jl:124 [7] create_synthetic_genotype(options::Dict{Any, Any}) @ Main /opt/intervene/scripts/algorithms/genotype/genotype_algorithm.jl:157 [8] macro expansion @ /opt/intervene/scripts/run_program.jl:31 [inlined] [9] macro expansion @ ./timing.jl:287 [inlined] [10] run_program(pipelines::Dict{String, Bool}, options::Dict{Any, Any}) @ Main /opt/intervene/scripts/run_program.jl:30 [11] main() @ Main /opt/intervene/scripts/run_program.jl:113 [12] top-level scope @ /opt/intervene/scripts/run_program.jl:117

nested task error: BoundsError: attempt to access 2-element Vector{Int64} at index [2]
Stacktrace:
 [1] setindex!
   @ ./array.jl:843 [inlined]
 [2] push!
   @ ./array.jl:934 [inlined]
 [3] is_threading(p::Progress)
   @ ProgressMeter ~/.julia/packages/ProgressMeter/sN2xr/src/ProgressMeter.jl:469
 [4] lock_if_threading
   @ ~/.julia/packages/ProgressMeter/sN2xr/src/ProgressMeter.jl:475 [inlined]
 [5] #next!#16
   @ ~/.julia/packages/ProgressMeter/sN2xr/src/ProgressMeter.jl:493 [inlined]
 [6] next!
   @ ~/.julia/packages/ProgressMeter/sN2xr/src/ProgressMeter.jl:493 [inlined]
 [7] macro expansion
   @ /opt/intervene/scripts/algorithms/genotype/write_output.jl:94 [inlined]
 [8] (::var"#857#threadsfor_fun#78"{DataFrame, Int64, GenomicMetadata, Progress, Dict{Int64, Matrix{Int8}}, UnitRange{Int64}})(onethread::Bool)
   @ Main ./threadingconstructs.jl:81
 [9] (::var"#857#threadsfor_fun#78"{DataFrame, Int64, GenomicMetadata, Progress, Dict{Int64, Matrix{Int8}}, UnitRange{Int64}})()
   @ Main ./threadingconstructs.jl:48

in expression starting at /opt/intervene/scripts/run_program.jl:117