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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.
The text was updated successfully, but these errors were encountered:
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:
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.
The text was updated successfully, but these errors were encountered: