timbitz
commented
5 years ago Hi @jordi-vaquero, to begin with-- 36nt is shorter than is generally recommended for Whippet, and caution should be used with data of such short read length.
In terms of your error, it is specifically because 36nt is just below the shortest read length allowed with the --bias flag engaged (which is 37nt). If you don't utilize the bias option then it should work, but again, this is still rather short. Currently the 36nt length is hard-coded in the bias models, and doesn't yet have a runtime parameter that can override those settings... I'm happy to consider this in a future version though.
Error trying to run psi quantification `ERROR: LoadError: BoundsError: attempt to access 35nt DNA Sequence: CGGGTGCTTTCTGCCCACCCCCTGCTCTTGCCAGC at index [31:36] Stacktrace:
[1] checkbounds(::BioSequences.BioSequence{BioSequences.DNAAlphabet{2}}, ::UnitRange{Int64}) at /home/jordi/.julia/v0.6/BioSequences/src/bioseq/indexing.jl:15
[2] BioSequences.BioSequence(::BioSequences.BioSequence{BioSequences.DNAAlphabet{2}}, ::UnitRange{Int64}) at /home/jordi/.julia/v0.6/BioSequences/src/bioseq/constructors.jl:33 [3] primer_count!(::Whippet.JointBiasMod, ::BioSequences.BioSequence{BioSequences.DNAAlphabet{2}}) at /home/jordi/.julia/v0.6/Whippet/src/bias.jl:163 [4] count! at /home/jordi/.julia/v0.6/Whippet/src/bias.jl:195 [inlined] [5] #process_paired_reads!#62(::Int64, ::Bool, ::Int64, ::Requests.ResponseStream{TCPSocket}, ::Requests.ResponseStream{TCPSocket}, ::Bool, ::Function, ::BioSequences.FASTQ.Reader, ::BioSequences.FASTQ.Reader, ::Whippet.AlignParam, ::Whippet.GraphLib, ::Whippet.GraphLibQuant{Whippet.SGAlignPaired,Whippet.JointBiasCounter}, ::Whippet.MultiMapping{Whippet.SGAlignPaired,Whippet.JointBiasCounter}, ::Whippet.JointBiasMod) at /home/jordi/.julia/v0.6/Whippet/src/reads.jl:160 [6] (::Whippet.#kw##process_paired_reads!)(::Array{Any,1}, ::Whippet.#process_paired_reads!, ::BioSequences.FASTQ.Reader, ::BioSequences.FASTQ.Reader, ::Whippet.AlignParam, ::Whippet.GraphLib, ::Whippet.GraphLibQuant{Whippet.SGAlignPaired,Whippet.JointBiasCounter}, ::Whippet.MultiMapping{Whippet.SGAlignPaired,Whippet.JointBiasCounter}, ::Whippet.JointBiasMod) at ./:0
[7] macro expansion at /home/jordi/.julia/v0.6/Whippet/src/timer.jl:5 [inlined]
[8] main() at /home/jordi/.julia/v0.6/Whippet/bin/whippet-quant.jl:169
[9] include_from_node1(::String) at ./loading.jl:576
[10] include(::String) at ./sysimg.jl:14
[11] process_options(::Base.JLOptions) at ./client.jl:305
[12] _start() at ./client.jl:371
while loading /home/jordi/.julia/v0.6/Whippet/bin/whippet-quant.jl, in expression starting on line 5`