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problem downloading scheme from pubmlst #122

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blooria opened this issue Nov 29, 2021 · 0 comments
Open

problem downloading scheme from pubmlst #122

blooria opened this issue Nov 29, 2021 · 0 comments

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@blooria
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blooria commented Nov 29, 2021

Hi,

I have a problem downloading both from pubmlst and cgmlst:
I have Julia 1.6, downloaded and installed manually, then tried the example:

src/mentalist download_pubmlst -k 31 -o campy_mlst_fasta_files -s 28 --db campy_mlst.db
ERROR: LoadError: LoadError: LoadError: On worker 2:
TypeError: in Type{...} expression, expected UnionAll, got Type{Mer{DNAAlphabet{2}, 31}}
Stacktrace:
[1] top-level scope
@ none:1
[2] eval
@ ./boot.jl:360
[3] #103
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Distributed/src/process_messages.jl:274
[4] run_work_thunk
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Distributed/src/process_messages.jl:63
[5] run_work_thunk
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Distributed/src/process_messages.jl:72
[6] #96
@ ./task.jl:411

...and 1 more exception.

Stacktrace:
[1] sync_end(c::Channel{Any})
@ Base ./task.jl:369
[2] macro expansion
@ ./task.jl:388 [inlined]
[3] remotecall_eval(m::Module, procs::Vector{Int64}, ex::Expr)
@ Distributed /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Distributed/src/macros.jl:223
[4] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Distributed/src/macros.jl:207
[5] include(fname::String)
@ Base.MainInclude ./client.jl:444
[6] top-level scope
@ ~/Desktop/MentaLiST-master/src/build_db_functions.jl:8
[7] include(fname::String)
@ Base.MainInclude ./client.jl:444
[8] top-level scope
@ ~/Desktop/MentaLiST-master/src/mentalist:345
in expression starting at /home/mor/Desktop/MentaLiST-master/src/db_graph.jl:12
in expression starting at /home/mor/Desktop/MentaLiST-master/src/build_db_functions.jl:8
in expression starting at /home/mor/Desktop/MentaLiST-master/src/mentalist:323

I also tried cgmlst for my chosen bacteria:
src/mentalist download_cgmlst --db acinetobacter -k 20 -o acinetobacter.db -s 3956907
ERROR: LoadError: LoadError: LoadError: TaskFailedException

nested task error: TypeError: in Type{...} expression, expected UnionAll, got Type{Mer{DNAAlphabet{2}, 31}}
Stacktrace:
 [1] top-level scope
   @ none:1
 [2] eval
   @ ./boot.jl:360 [inlined]
 [3] (::Distributed.var"#155#156"{Module, Expr})()
   @ Distributed ./task.jl:411

Stacktrace:
[1] sync_end(c::Channel{Any})
@ Base ./task.jl:369
[2] macro expansion
@ ./task.jl:388 [inlined]
[3] remotecall_eval(m::Module, procs::Vector{Int64}, ex::Expr)
@ Distributed /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Distributed/src/macros.jl:223
[4] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Distributed/src/macros.jl:207
[5] include(fname::String)
@ Base.MainInclude ./client.jl:444
[6] top-level scope
@ ~/Desktop/MentaLiST-master/src/build_db_functions.jl:8
[7] include(fname::String)
@ Base.MainInclude ./client.jl:444
[8] top-level scope
@ ~/Desktop/MentaLiST-master/src/mentalist:357
in expression starting at /home/mor/Desktop/MentaLiST-master/src/db_graph.jl:12
in expression starting at /home/mor/Desktop/MentaLiST-master/src/build_db_functions.jl:8
in expression starting at /home/mor/Desktop/MentaLiST-master/src/mentalist:323

any help will be appreciated

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