ERROR: LoadError: BoundsError: attempt to access 2-element Array{Whippet.SGAlignNode,1} at index

[amitfenn]

Thank you Dr Sterne-Weiler, for making Whippet, I really like this tool and I love the simple outputs it brings me, while staying pretty precise.

I have to ask you about this error, because with the same script, I was able to process 16/38 samples, but 22 of them seem to have an error that's similar to this. Please reach out to me for more debugging info.

My current set up is a little unusual, I have a docker container that hosts whippet. But unless you're doing some cgroup magic, i don't think that should matter so much.

Whippet v0.11.1 loading and compiling... 
 13.226979 seconds
Loading splice graph index... /MOUNT/output/whippet-output/21Mar37559_A05-L1_S5_R_starAligned.out_output/graph.jls
 10.380433 seconds (8.64 M allocations: 2.328 GiB, 12.91% gc time)
Processing reads from file...
FASTQ_1: /MOUNT/input/controldir/fastqdir/21Mar37559_A05-L1_S5_R1.fastq
FASTQ_2: /MOUNT/input/controldir/fastqdir/21Mar37559_A05-L1_S5_R2.fastq
ERROR: LoadError: BoundsError: attempt to access 2-element Array{Whippet.SGAlignNode,1} at index [3]
Stacktrace:
 [1] #ungapped_fwd_extend#45(::Bool, ::Whippet.SGAlignment, ::UInt32, ::Function, ::Whippet.AlignParam, ::Whippet.GraphLib, ::UInt32, ::Int64, ::Whippet.FASTQRecord, ::Int64) at /opt/.julia/v0.6/Whippet/src/align.jl:389
 [2] (::Whippet.#kw##ungapped_fwd_extend)(::Array{Any,1}, ::Whippet.#ungapped_fwd_extend, ::Whippet.AlignParam, ::Whippet.GraphLib, ::UInt32, ::Int64, ::Whippet.FASTQRecord, ::Int64) at ./<missing>:0
 [3] #_ungapped_align#43 at /opt/.julia/v0.6/Whippet/src/align.jl:214 [inlined]
 [4] (::Whippet.#kw##_ungapped_align)(::Array{Any,1}, ::Whippet.#_ungapped_align, ::Whippet.AlignParam, ::Whippet.GraphLib, ::Whippet.FASTQRecord, ::Int64, ::Int64) at ./<missing>:0
 [5] #ungapped_align#63(::Bool, ::Bool, ::Function, ::Whippet.AlignParam, ::Whippet.GraphLib, ::Whippet.FASTQRecord, ::Whippet.FASTQRecord) at /opt/.julia/v0.6/Whippet/src/paired.jl:80
 [6] #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.DefaultCounter}, ::Whippet.MultiMapping{Whippet.SGAlignPaired,Whippet.DefaultCounter}, ::Whippet.DefaultBiasMod) at /opt/.julia/v0.6/Whippet/src/reads.jl:158
 [7] (::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.DefaultCounter}, ::Whippet.MultiMapping{Whippet.SGAlignPaired,Whippet.DefaultCounter}, ::Whippet.DefaultBiasMod) at ./<missing>:0
 [8] macro expansion at /opt/.julia/v0.6/Whippet/src/timer.jl:5 [inlined]
 [9] main() at /docker_main/bin/whippet-quant.jl:169
 [10] include_from_node1(::String) at ./loading.jl:576
 [11] include(::String) at ./sysimg.jl:14
 [12] process_options(::Base.JLOptions) at ./client.jl:305
 [13] _start() at ./client.jl:371
while loading /docker_main/bin/whippet-quant.jl, in expression starting on line 5

[timbitz]

Hi @amitfenn, this is a duplicate of #79 -- I actually haven't been able to reproduce this, but I'm fairly certain its related to the building of your index (are you using the --suppress-low-tsl option?). I'm still happy to fix this bug for this version, but you'll need to provide a small reproducible set of inputs (example index files, and the offending fastq lines).

[amitfenn]

Sorry, Dr Sterne-Weiler, I won't be able to help you, because the data that is under GDPR protection. I am able to use whippet on another dataset and will continue to work there. It's still awesome that you already suspect what the bug is.

Thanks for your time.