Load error when creating db from cgmlst

[andersgs]

Hi.

I installed MentaLiST using Bioconda:

conda install -c conda-forge -c bioconda -c defaults mentalist==0.2.4

I then tried running the following:

mentalist download_cgmlst --db /opt/db/efaec_cgmlst.db -k 31 -o /opt/db/efaec_cgmlst_fasta -s 991893 --threads 2

It shoots out a lot of WARNINGS, but then eventually crashes out with the following:

ERROR: LoadError: LoadError: LoadError: MethodError: no method matching convert(::Type{AssertionError}, ::String)
Closest candidates are:
  convert(!Matched::Type{Any}, ::ANY) at essentials.jl:28
  convert(::Type{T}, !Matched::T) where T at essentials.jl:29
AssertionError(::String) at ./coreimg.jl:14
update_valid_age!(::UInt64, ::UInt64, ::Core.Inference.InferenceState) at ./inference.jl:2353
add_backedge!(::Core.MethodInstance, ::Core.Inference.InferenceState) at ./inference.jl:2366
abstract_call_gf_by_type(::Any, ::Any, ::Core.Inference.InferenceState) at ./inference.jl:1421
abstract_call(::Any, ::Array{Any,1}, ::Array{Any,1}, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1897
abstract_eval_call(::Expr, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1927
abstract_eval(::Any, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1950
abstract_interpret(::Any, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:2084
typeinf_work(::Core.Inference.InferenceState) at ./inference.jl:2669
typeinf(::Core.Inference.InferenceState) at ./inference.jl:2787
typeinf_edge(::Method, ::Any, ::SimpleVector, ::Core.Inference.InferenceState) at ./inference.jl:2535
abstract_call_gf_by_type(::Any, ::Any, ::Core.Inference.InferenceState) at ./inference.jl:1420
abstract_call(::Any, ::Array{Any,1}, ::Array{Any,1}, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1897
abstract_eval_call(::Expr, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1927
abstract_eval(::Any, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1950
abstract_interpret(::Any, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:2084
typeinf_work(::Core.Inference.InferenceState) at ./inference.jl:2669
typeinf(::Core.Inference.InferenceState) at ./inference.jl:2787
typeinf_edge(::Method, ::Any, ::SimpleVector, ::Core.Inference.InferenceState) at ./inference.jl:2535
abstract_call_gf_by_type(::Any, ::Any, ::Core.Inference.InferenceState) at ./inference.jl:1420
abstract_call(::Any, ::Array{Any,1}, ::Array{Any,1}, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1897
abstract_eval_call(::Expr, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1927
abstract_eval(::Any, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1950
typeinf_work(::Core.Inference.InferenceState) at ./inference.jl:2722
typeinf(::Core.Inference.InferenceState) at ./inference.jl:2787
typeinf_edge(::Method, ::Any, ::SimpleVector, ::Core.Inference.InferenceState) at ./inference.jl:2535
abstract_call_gf_by_type(::Any, ::Any, ::Core.Inference.InferenceState) at ./inference.jl:1420
abstract_call(::Any, ::Array{Any,1}, ::Array{Any,1}, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1897
abstract_eval_call(::Expr, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1927
abstract_eval(::Any, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1950
abstract_interpret(::Any, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:2084
typeinf_work(::Core.Inference.InferenceState) at ./inference.jl:2669
typeinf(::Core.Inference.InferenceState) at ./inference.jl:2787
typeinf_edge(::Method, ::Any, ::SimpleVector, ::Core.Inference.InferenceState) at ./inference.jl:2535
abstract_call_gf_by_type(::Any, ::Any, ::Core.Inference.InferenceState) at ./inference.jl:1420
abstract_call(::Any, ::Tuple{}, ::Array{Any,1}, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1897
abstract_apply(::Any, ::Array{Any,1}, ::Array{Any,1}, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1561
abstract_call(::Any, ::Array{Any,1}, ::Array{Any,1}, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1689
abstract_eval_call(::Expr, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1927
abstract_eval(::Any, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1950
typeinf_work(::Core.Inference.InferenceState) at ./inference.jl:2722
typeinf(::Core.Inference.InferenceState) at ./inference.jl:2787
typeinf_edge(::Method, ::Any, ::SimpleVector, ::Core.Inference.InferenceState) at ./inference.jl:2535
abstract_call_gf_by_type(::Any, ::Any, ::Core.Inference.InferenceState) at ./inference.jl:1420
abstract_call(::Any, ::Tuple{}, ::Array{Any,1}, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1897
abstract_apply(::Any, ::Array{Any,1}, ::Array{Any,1}, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1561
abstract_call(::Any, ::Array{Any,1}, ::Array{Any,1}, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1689
abstract_eval_call(::Expr, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1927
abstract_eval(::Any, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1950
typeinf_work(::Core.Inference.InferenceState) at ./inference.jl:2722
typeinf(::Core.Inference.InferenceState) at ./inference.jl:2787
typeinf_edge(::Method, ::Any, ::SimpleVector, ::Core.Inference.InferenceState) at ./inference.jl:2535
abstract_call_gf_by_type(::Any, ::Any, ::Core.Inference.InferenceState) at ./inference.jl:1420
abstract_call(::Any, ::Tuple{}, ::Array{Any,1}, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1897
abstract_apply(::Any, ::Array{Any,1}, ::Array{Any,1}, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1561
abstract_call(::Any, ::Array{Any,1}, ::Array{Any,1}, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1689
abstract_eval_call(::Expr, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1927
abstract_eval(::Any, ::Array{Any,1}, ::Core.Inference.InferenceState) at ./inference.jl:1950
typeinf_work(::Core.Inference.InferenceState) at ./inference.jl:2722
typeinf(::Core.Inference.InferenceState) at ./inference.jl:2787
typeinf_frame(::Core.MethodInstance, ::Bool, ::Bool, ::Core.Inference.InferenceParams) at ./inference.jl:2504
typeinf_code(::Core.MethodInstance, ::Bool, ::Bool, ::Core.Inference.InferenceParams) at ./inference.jl:2583
typeinf_ext(::Core.MethodInstance, ::UInt64) at ./inference.jl:2622
macro expansion at ./loading.jl:180 [inlined]
(::Base.##691#693)() at ./task.jl:335

...and 1 more exception(s).

Stacktrace:
 [1] sync_end() at ./task.jl:287
 [2] macro expansion at ./task.jl:303 [inlined]
 [3] _require_from_serialized(::Int64, ::Symbol, ::String, ::Bool) at ./loading.jl:177
 [4] _require(::Symbol) at ./loading.jl:498
 [5] require(::Symbol) at ./loading.jl:405
 [6] include_from_node1(::String) at ./loading.jl:576
 [7] include(::String) at ./sysimg.jl:14
 [8] include_from_node1(::String) at ./loading.jl:576
 [9] include(::String) at ./sysimg.jl:14
 [10] include_from_node1(::String) at ./loading.jl:576
 [11] include(::String) at ./sysimg.jl:14
 [12] process_options(::Base.JLOptions) at ./client.jl:305
 [13] _start() at ./client.jl:371
while loading /opt/conda/bin/db_graph.jl, in expression starting on line 2
while loading /opt/conda/bin/build_db_functions.jl, in expression starting on line 6
while loading /opt/conda/bin/mentalist, in expression starting on line 314
MethodError(Core.Inference.convert, (AssertionError, "invalid age range update"), 0x0000000000000ac6)

I am running version 0.2.4.

I am building a Docker container with MentaLiST and the DB contained within it. The Dockerfile pasted below.

Thank you.

Anders.

FROM continuumio/miniconda:4.7.12 as build

RUN apt-get --yes update && apt-get --yes upgrade && apt-get clean

RUN conda update conda && conda install -c conda-forge -c bioconda -c defaults mentalist==0.2.4

RUN mkdir /opt/db && mentalist download_cgmlst --db /opt/db/efaec_cgmlst.db -k 31 -o /opt/db/efaec_cgmlst_fasta -s 991893 --threads 2

FROM build

COPY --from=build /opt/conda /opt/conda 
COPY --from=build /opt/db /opt/db

CMD [ "mentalist call --db /opt/db/efaec_cgmlst.db" ]