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Error during genotype generation #30

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bruno-ariano opened this issue Jan 19, 2024 · 0 comments
Open

Error during genotype generation #30

bruno-ariano opened this issue Jan 19, 2024 · 0 comments

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@bruno-ariano
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bruno-ariano commented Jan 19, 2024

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: 0:00:16�[KERROR:
LoadError: Progress: 91%|█████████████████████████████████████▎ | ETA: 0:00:16TaskFailedException�[K

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

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