Dear All,

I encountered an error while running whippet-index.jl. The error appears to be due to my GTF file not being in the 2.2 format. Could you please let me know where to download the correct GTF format (GTF2.2) for hg38? The link provided on this website does not work. Is there an updated link available?

Thank you,

Xiao

PS: error messages:
(base) xiaolei@Xiaos-Laptop bin % julia ./whippet-index.jl --fasta /Users/xiaolei/Whippet.jl/anno/hg38.fa.gz --gtf /Users/xiaolei/Whippet.jl/anno/gencode.v45.annotation_sorted.gtf.gz
Whippet v1.6.2 loading...
Activating environment at ~/Whippet.jl/Project.toml
5.640663 seconds.
Loading GTF file: /Users/xiaolei/Whippet.jl/anno/gencode.v45.annotation_sorted.gtf.gz

┌ Warning: Using low quality Transcript Support Levels (TSL 3+) in your GTF file is not recommended!
│ For more information on TSL, see: http://www.ensembl.org/Help/Glossary?id=492
│
│ If you would like Whippet to ignore these when building its index, use --suppress-low-tsl option!
│
└ @ Whippet ~/Whippet.jl/src/refset.jl:159
ERROR: LoadError: ERROR: GTF file is not in valid GTF2.2 format!

ERROR: Annotation entries for 'transcript_id' ENST00000430923.7 has already been fully processed and closed.
HINT: All GTF lines with the same 'transcript_id' must be adjacent in the GTF file and referring to the same transcript and gene!
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] load_gtf(fh::BufferedStreams.BufferedInputStream{Libz.Source{:inflate, BufferedStreams.BufferedInputStream{IOStream}}}; txbool::Bool, suppress::Bool, usebam::Bool, bamreader::Nullable{XAM.BAM.Reader}, bamreads::Int64, bamoneknown::Bool)
@ Whippet ~/Whippet.jl/src/refset.jl:165
[3] macro expansion
@ ~/Whippet.jl/src/timer.jl:5 [inlined]
[4] main()
@ Main ~/Whippet.jl/bin/whippet-index.jl:91
[5] top-level scope
@ ~/Whippet.jl/src/timer.jl:5
in expression starting at /Users/xiaolei/Whippet.jl/bin/whippet-index.jl:108