Issue with BioSequences

[zoescherzer0318]

I left a previous issue detailing my struggles but I have updated the Julia version and managed to sort through those errors. Now I am getting a new error (below). I ran pkg> test and all worked out. I am wondering if this new error has something to do with my fastq files (single-end).

c26a-s28.ufhpc Thu Aug 18 14:40:29 EDT 2022 Working directory is /blue/ewang/zoejstar/libZJS module add julia cd ~/julia-1.7.3/Whippet.jl/ julia ~/julia-1.7.3/Whippet.jl/bin/whippet-quant.jl /blue/ewang/zoejstar/NIH3T3/fasta_files/SRR1816794_1.fastq.gz -o /blue/ew ang/zoejstar/NIH3T3/whippet_output/3T3_1 -x /home/zoejstar/julia-1.7.3/Whippet.jl/index/graph.jls Whippet v1.6.1 loading... Activating project at ~/julia-1.7.3/Whippet.jl 16.472457 seconds. Loading splice graph index... /home/zoejstar/julia-1.7.3/Whippet.jl/index/graph.jls 2.593315 seconds (3.27 M allocations: 568.733 MiB, 21.99% gc time) Processing reads from file... FASTQ: /blue/ewang/zoejstar/NIH3T3/fasta_files/SRR1816794_1.fastq.gz ERROR: LoadError: Cannot encode 78 to BioSequences.DNAAlphabet{2}() Stacktrace: [1] error(s::String) @ Base ./error.jl:33 [2] throw_encode_error(A::BioSequences.DNAAlphabet{2}, src::Vector{UInt8}, soff::Int64) @ BioSequences ~/.julia/packages/BioSequences/k4j4J/src/longsequences/copying.jl:216 [3] encode_chunk @ ~/.julia/packages/BioSequences/k4j4J/src/longsequences/copying.jl:228 [inlined] [4] encode_chunks!(dst::BioSequences.LongSequence{BioSequences.DNAAlphabet{2}}, startindex::Int64, src::Vector{UInt8}, soff::Int64, N::Int64) @ BioSequences ~/.julia/packages/BioSequences/k4j4J/src/longsequences/copying.jl:239 [5] copyto!(dst::BioSequences.LongSequence{BioSequences.DNAAlphabet{2}}, doff::Int64, src::Vector{UInt8}, soff::Int64, N::Int64, #unused#::BioSequences.AsciiAlphabet) @ BioSequences ~/.julia/packages/BioSequences/k4j4J/src/longsequences/copying.jl:361 [6] copyto! @ ~/.julia/packages/BioSequences/k4j4J/src/longsequences/copying.jl:292 [inlined] [7] BioSequences.LongSequence{BioSequences.DNAAlphabet{2}}(src::Vector{UInt8}, startpos::Int64, stoppos::Int64) @ BioSequences ~/.julia/packages/BioSequences/k4j4J/src/longsequences/constructors.jl:49 [8] BioSequence @ ~/julia-1.7.3/Whippet.jl/src/types.jl:74 [inlined] [9] fill!(rec::Whippet.FASTQRecord, offset::Int64) @ Whippet ~/julia-1.7.3/Whippet.jl/src/record.jl:14 [10] process_reads!(parser::FASTX.FASTQ.Reader{TranscodingStreams.NoopStream{BufferedStreams.BufferedInputStream{Libz.Source{:inflate, BufferedStreams.BufferedInputStream{IOStream}}}}}, param::AlignParam, lib::GraphLib, quant::GraphLibQuant{SGAlignSingle, DefaultCounter}, multi::MultiMapping{SGAlignSingle, DefaultCounter}, mod::DefaultBiasMod; bufsize::Int64, sam::Bool, qualoffset::Int64) @ Whippet ~/julia-1.7.3/Whippet.jl/src/reads.jl:57 [11] macro expansion @ ~/julia-1.7.3/Whippet.jl/src/timer.jl:5 [inlined] [12] main() @ Main ~/julia-1.7.3/Whippet.jl/bin/whippet-quant.jl:149 [13] top-level scope @ ~/julia-1.7.3/Whippet.jl/src/timer.jl:5 in expression starting at /home/zoejstar/julia-1.7.3/Whippet.jl/bin/whippet-quant.jl:185 ===== module add julia cd ~/julia-1.7.3/Whippet.jl/ julia ~/julia-1.7.3/Whippet.jl/bin/whippet-quant.jl /blue/ewang/zoejstar/NIH3T3/fasta_files/SRR1816794_1.fastq.gz -o /blue/ewang/zoejstar/NIH3T3/whippet_output/3T3_1 -x /home/zoejstar/julia-1.7.3/Whippet.jl/index/graph.jls finished ===== (END)

[zoescherzer0318]

Nevermind, I found the answer in previous errors submitted.

[nick-webster]

Hi Zoe, I have a similar issue. What was the solution? I looked through earlier errors but couldn't find anything relevant. Thanks, Nick

[timbitz]

The answer is in #118

"Whippet only accepts as input the standard four-line FASTQ file (described here: https://support.illumina.com/bulletins/2016/04/fastq-files-explained.html). The extra name id after the '+' is the problem. This is a standard expectation, but I'll update the documentation to reflect this."