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Error building MentaLiST database from Enterobase schema #101

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glwinsor opened this issue Mar 28, 2019 · 0 comments
Open

Error building MentaLiST database from Enterobase schema #101

glwinsor opened this issue Mar 28, 2019 · 0 comments

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@glwinsor
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I’m having a problem installing a wgMLST schema on SFU’s galaxy instance. When attempting to install the Enterobase E.coli/Shigella wgMLST schema, I get this error:

WARNING: imported binding for VERSION overwritten in module Main
ERROR: LoadError: error parsing fastaparser input on line 1
 in read!(::Bio.Seq.FASTAReader{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}}}, ::Bio.Seq.SeqRecord{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}},Bio.Seq.FASTAMetadata}) at /project/6004808/irida/galaxy-tool-dependencies/_conda/envs/[email protected]/share/julia/site/v0.5/Bio/src/Ragel.jl:178
 in (::##17#18{31,Set{Bio.Seq.Kmer{Bio.Seq.DNANucleotide,31}},Bio.Seq.SeqRecord{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}},Bio.Seq.FASTAMetadata}})(::Bio.Seq.FASTAReader{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}}}) at /project/6004808/irida/galaxy-tool-dependencies/_conda/envs/[email protected]/bin/db_graph.jl:14
 in #open#1(::Array{Any,1}, ::Function, ::##17#18{31,Set{Bio.Seq.Kmer{Bio.Seq.DNANucleotide,31}},Bio.Seq.SeqRecord{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}},Bio.Seq.FASTAMetadata}}, ::Type{Bio.Seq.FASTAReader{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}}}}, ::String, ::Vararg{String,N}) at /project/6004808/irida/galaxy-tool-dependencies/_conda/envs/[email protected]/share/julia/site/v0.5/Bio/src/IO.jl:41
 in build(::Type{Bio.Seq.Kmer{Bio.Seq.DNANucleotide,31}}, ::Array{String,1}) at /project/6004808/irida/galaxy-tool-dependencies/_conda/envs/[email protected]/bin/db_graph.jl:12
 in db_graph_contig_kmers(::Type{Bio.Seq.Kmer{Bio.Seq.DNANucleotide,31}}, ::Array{String,1}) at /project/6004808/irida/galaxy-tool-dependencies/_conda/envs/[email protected]/bin/db_graph.jl:81
 in kmer_class_for_locus(::Type{Bio.Seq.Kmer{Bio.Seq.DNANucleotide,31}}, ::String, ::Bool) at /project/6004808/irida/galaxy-tool-dependencies/_conda/envs/[email protected]/bin/build_db_functions.jl:123
 in kmer_class_for_each_locus(::Int8, ::Array{String,1}, ::Bool) at /project/6004808/irida/galaxy-tool-dependencies/_conda/envs/[email protected]/bin/build_db_functions.jl:113
 in build_db(::Dict{String,Any}, ::String) at /project/6004808/irida/galaxy-tool-dependencies/_conda/envs/[email protected]/bin/mentalist:221
 in download_enterobase(::Dict{String,Any}) at /project/6004808/irida/galaxy-tool-dependencies/_conda/envs/[email protected]/bin/mentalist:213
 in main() at /project/6004808/irida/galaxy-tool-dependencies/_conda/envs/[email protected]/bin/mentalist:248
 in include_from_node1(::String) at ./loading.jl:488
 in process_options(::Base.JLOptions) at ./client.jl:265
 in _start() at ./client.jl:321
while loading /project/6004808/irida/galaxy-tool-dependencies/_conda/envs/[email protected]/bin/mentalist, in expression starting on line 252
Error building database.

I'm using MentaLiST 0.1.9 and Galaxy version 17.09.

I hear that Enterobase E.coli/Shigella has been successfully built before so the current problem could possibly be related to unexpected characters in the most recent schema file.

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