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Hi all,
I am trying to use Flux Simulator with a .gtf file from Illumina's iGenomes collection.  = ;Specifically, I am using the genes.gtf in the Drosophila_melanogaster= /UCSC/dm3/Annotation/Genes subdirectory of this archive: dm3. I have set REF_FILE_NAME appropriately. = However, when I run flux-simulator, I get an warning indicating that the GT= F file isn't sorted. Next, flux "sorts" the GTF file for me, but then= yields an error saying that the sorted file isn't sorted:
$ ./flux-simulator/bin/flux-simulator -p parameters/example.par
Fl= ux-Simulator v1.2.1 (Flux Library: 1.22)
[INFO] No mode selected, executing the full pipeline (-x -l -s)
[IN= FO] I am collecting information on the run.
[INFO] Reading error model 7= 6 bases model
[INFO] Checking GTF file
Checking GTF *[WARN] Unsorted in line 4 t= ranscript id NM_175941 used twice, on: chr2L,chr2L
[GTF FILE] The GTF re= ference file given is not sorted, sorting it right now...
sorting GTF f= ile OK (00:00:20)
[GTF FILE] The Simulator will use /Users/langmead/git/= tornado/tools/flux_sim/parameters/genes_sorted.gtf
[GTF FILE] You might = want to update your parameters file
[PROFILING] I am assigning the expre= ssion profile
Checking GTF *[WARN] Unsorted in line 3496 transcript id = NR_073697 used twice, on: chr2L,chr2L
[ERROR] The reference annotation GTF is not sorted!
java.lang.R= untimeException: The reference annotation GTF is not sorted!
at barna.f= lux.simulator.Profiler.createGTFReader(Profiler.java:756)
at barna.flux.s= imulator.Profiler.readAnnotation(Profiler.java:202)
at barna.flux.simulat= or.Profiler.call(Profiler.java:127)
at barna.flux.simulator.SimulationPip= eline.call(SimulationPipeline.java:429)
at barna.flux.simulator.Simulatio= nPipeline.call(SimulationPipeline.java:54)
at barna.commons.launcher.Fl= ux.main(Flux.java:198)
I'm guessing this has something to do with how the .gtf files from iGeno= mes are formatted. Apparently, they are formatted to contain informat= ion that Cufflinks likes so that it can do differential analysis w/r/t prom= oters and coding sequences, in addition to transcripts:
http://cufflinks.cbcb.umd.edu/igenomes.html
Can you help?
Best,
Ben