ERROR: LoadError: BoundsError: attempt to access BioSequences.LongDNASeq at index [65269405:65269446] #141
Description
Hi,
I am getting some error when running Whippet-index.jl, where it complains that it is out of bounds, even though it should still be within the the reference genome:
julia Whippet.jl/bin/whippet-index.jl --fasta ../../S_lycopersicum_chromosomes.4.00.fa --gtf test2.gtf -x ../../whippet_unique_transcriptome_events
Whippet v1.6.2 loading...
Activating project at ~/Whippet.jl
16.266195 seconds.
Loading GTF file: /root/test2.gtf
Loaded 471656 annotated splice-sites from GTF file..
164.124672 seconds (154.92 M allocations: 11.094 GiB, 2.60% gc time)
Indexing transcriptome...
Indexing /S_lycopersicum_chromosomes.4.00.fa...
Building Splice Graphs for SL4.0ch00..
3.113879 seconds (17.48 M allocations: 2.086 GiB, 22.73% gc time)
Building Splice Graphs for SL4.0ch01..
21.870180 seconds (84.81 M allocations: 47.234 GiB, 7.50% gc time)
Building Splice Graphs for SL4.0ch02..
31.897106 seconds (72.50 M allocations: 74.254 GiB, 5.38% gc time)
Building Splice Graphs for SL4.0ch03..
57.063836 seconds (67.03 M allocations: 113.639 GiB, 5.28% gc time)
Building Splice Graphs for SL4.0ch04..
74.869988 seconds (50.37 M allocations: 132.843 GiB, 5.17% gc time)
Building Splice Graphs for SL4.0ch05..
ERROR: LoadError: BoundsError: attempt to access BioSequences.LongDNASeq at index [65269405:65269446]
Stacktrace:
[1] checkbounds
The reference genome has a few bp more then what seems to be indexed:
##sequence-regionSL4.0ch05 1 65269487
I have looked at the other error reports concerning BoundsErrors, but I think this one is unrelated.
Best,
David