Running whippet-quant.jl on single end sample didn't work. (It always worked well for paired end)
run julia /home/luco/soft/Whippet.jl-0.10.4/bin/whippet-quant.jl -x /home/luco/index_whippet/human/human_index_whippet_10.0.4 /home/luco/work/nrf2_rbm47/fastq/29_1.fastq.gz -o /home/luco/work/nrf2_rbm47/output/29
ERROR: LoadError: InexactError()
Stacktrace:
[1] #seed_locate#44 at /home/luco/.julia/v0.6/Whippet/src/align.jl:147 [inlined]
[2] (::Whippet.#kw##seed_locate)(::Array{Any,1}, ::Whippet.#seed_locate, ::Whippet.AlignParam, ::FMIndexes.FMIndex{2,UInt32}, ::Whippet.FASTQRecord) at ./<missing>:0
[3] #ungapped_align#46 at /home/luco/.julia/v0.6/Whippet/src/align.jl:229 [inlined]
[4] ungapped_align at /home/luco/.julia/v0.6/Whippet/src/align.jl:229 [inlined]
[5] #process_reads!#63(::Int64, ::Bool, ::Int64, ::Requests.ResponseStream{TCPSocket}, ::Bool, ::Function, ::BioSequences.FASTQ.Reader, ::Whippet.AlignParam, ::Whippet.GraphLib, ::Whippet.GraphLibQuant{Whippet.SGAlignSingle,Whippet.DefaultCounter}, ::Whippet.MultiMapping{Whippet.SGAlignSingle,Whippet.DefaultCounter}, ::Whippet.DefaultBiasMod) at /home/luco/.julia/v0.6/Whippet/src/reads.jl:104
[6] (::Whippet.#kw##process_reads!)(::Array{Any,1}, ::Whippet.#process_reads!, ::BioSequences.FASTQ.Reader, ::Whippet.AlignParam, ::Whippet.GraphLib, ::Whippet.GraphLibQuant{Whippet.SGAlignSingle,Whippet.DefaultCounter}, ::Whippet.MultiMapping{Whippet.SGAlignSingle,Whippet.DefaultCounter}, ::Whippet.DefaultBiasMod) at ./<missing>:0
[7] macro expansion at /home/luco/.julia/v0.6/Whippet/src/timer.jl:5 [inlined]
[8] main() at /home/luco/soft/Whippet.jl-0.10.4/bin/whippet-quant.jl:177
[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/luco/soft/Whippet.jl-0.10.4/bin/whippet-quant.jl, in expression starting on line 5
Hi,,
Running whippet-quant.jl on single end sample didn't work. (It always worked well for paired end)
run julia /home/luco/soft/Whippet.jl-0.10.4/bin/whippet-quant.jl -x /home/luco/index_whippet/human/human_index_whippet_10.0.4 /home/luco/work/nrf2_rbm47/fastq/29_1.fastq.gz -o /home/luco/work/nrf2_rbm47/output/29
Dataset I tried to analyse is here : https://www.ebi.ac.uk/ena/data/search?query=PRJNA262663+
Download several times the fastq, still same error. Any idea ?