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timbitz / Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level
MIT License
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whippet-quant.jl error #104

Closed JamalEH closed 2 years ago

JamalEH commented 4 years ago

I got the following error when I was running Whippet on my dataset. the RNA-Seq dataset is paired end of 75bp length and about 60M reads in depth per library. Please help me to set this issue. command line used: whippet-quant.jl ../SRR10992916_1.fastq.gz ../SRR10992916_2.fastq.gz -x ./graph.jls -o ./SRR10992916 --biascorrect &

Loading splice graph index... /vol1/Analysis/DeBortoli/RNASeq_Noncoding_LNA_siRNA/GSE144580/whippet/graph.jls 23.727009 seconds (7.85 M allocations: 997.998 MiB, 9.51% gc time) Processing reads from file... FASTQ_1: /vol1/Analysis/DeBortoli/RNASeq_Noncoding_LNA_siRNA/GSE144580/SRR10992916_1.fastq.gz FASTQ_2: /vol1/Analysis/DeBortoli/RNASeq_Noncoding_LNA_siRNA/GSE144580/SRR10992916_2.fastq.gz ERROR: LoadError: BoundsError: attempt to access 35nt DNA Sequence: TTTTTTCTCGAGGACCCCCCTGGGGCCCCCCACAC at index [31:36] Stacktrace: [1] checkbounds(::BioSequences.BioSequence{BioSequences.DNAAlphabet{2}}, ::UnitRange{Int64}) at /home/jelhasnaoui/.julia/v0.6/BioSequences/src/bioseq/indexi ng.jl:15 [2] BioSequences.BioSequence(::BioSequences.BioSequence{BioSequences.DNAAlphabet{2}}, ::UnitRange{Int64}) at /home/jelhasnaoui/.julia/v0.6/BioSequences/src/ bioseq/constructors.jl:33 [3] primer_count!(::Whippet.JointBiasMod, ::BioSequences.BioSequence{BioSequences.DNAAlphabet{2}}) at /home/jelhasnaoui/.julia/v0.6/Whippet/src/bias.jl:163 [4] count! at /home/jelhasnaoui/.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, ::Bi oSequences.FASTQ.Reader, ::BioSequences.FASTQ.Reader, ::Whippet.AlignParam, ::Whippet.GraphLib, ::Whippet.GraphLibQuant{Whippet.SGAlignPaired,Whippet.JointBi asCounter}, ::Whippet.MultiMapping{Whippet.SGAlignPaired,Whippet.JointBiasCounter}, ::Whippet.JointBiasMod) at /home/jelhasnaoui/.julia/v0.6/Whippet/src/read s.jl:160 [6] (::Whippet.#kw##process_paired_reads!)(::Array{Any,1}, ::Whippet.#process_paired_reads!, ::BioSequences.FASTQ.Reader, ::BioSequences.FASTQ.Reader, ::Whi ppet.AlignParam, ::Whippet.GraphLib, ::Whippet.GraphLibQuant{Whippet.SGAlignPaired,Whippet.JointBiasCounter}, ::Whippet.MultiMapping{Whippet.SGAlignPaired,Wh ippet.JointBiasCounter}, ::Whippet.JointBiasMod) at ./:0 [7] macro expansion at /home/jelhasnaoui/.julia/v0.6/Whippet/src/timer.jl:5 [inlined] [8] main() at /home/jelhasnaoui/.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/jelhasnaoui/.julia/v0.6/Whippet/bin/whippet-quant.jl, in expression starting on line 5

Thank you so much in advance! Best regards, Jamal.

JamalEH commented 4 years ago

The error mentioned above is occuring only when the "--biascorrect" option is included in the command. Removing it those not produce any error.

Best regards, Jamal.

timbitz commented 2 years ago

Repeat of #85