Not all HaploDup reports knit to html

[BaxW]

I'm running haploDup on a diploid assembly for an organism with 19 chromosomes. My command line looks like:

HaploDup.py \
            -f hap1.fasta,hap2.fasta \
            -g hap1.gff,hap2.gff \
            -c cor.txt \
	     -o haplodup_ver_939 \
            -t 32 \
            -r guide.hardmasked.fa \
            -a guide.gene.gff

but when I look in haplodup_ver_939.HaploDup_dir/Hap1_vs_Hap2/ there is a pdf version of the report for alignments of all 19 chromosomes, but there is only an html version of the report for chromosomes 14-19. I would rather have the html version so that I can zoom in on regions of interest.

To troubleshoot, I've tried running an individual rmarkdown::render() command for just one of the html reports that is missing like this:

         Rscript -e 'library(rmarkdown) ; rmarkdown::render("/gpfs1/home/b/w/bwworthi/myapps/HaploSync/lib_files/../support_scripts/ChrBoard.html.nostructure.nolegacy.nomarkers.Rmd" , knit_root_dir = "/netfiles02/pophyb/balsamRef/haplodup_ver_939.HaploDup_dir" , output_file = "haplosyn_ver_939_Hap1_Chr03.on.haplosyn_ver_939_Hap2_Chr03.report.html" , output_dir = "/netfiles02/pophyb/balsamRef/haplodup_ver_939.HaploDup_dir/Hap1_vs_Hap2" , params=list(coords = "Hap1.on.Hap2.coords.txt" , coords_self = "Hap2.on.Hap2.coords.txt" , counts_hap1 = "diploid_gene_count_trace.hap1.txt" , counts_hap2 = "diploid_gene_count_trace.hap2.txt" , min_align = "3000" , similarity = "90" , queryID = "haplosyn_ver_939_Hap1_Chr03" , refID = "haplosyn_ver_939_Hap2_Chr03" , hap1ID = "haplosyn_ver_939_Hap1_Chr03" , hap2ID = "haplosyn_ver_939_Hap2_Chr03" , hap1Len = "29296493" , hap2Len = "15254741" , ratio= "0.33" , structure = "" , legacy = "" , markers = "" , dup_markers = "" ))'

but I get this error:

Quitting from lines 288-328 (ChrBoard.html.nostructure.nolegacy.nomarkers.Rmd) 
Error in seq.default(min(diploid_trace11$count), max(diploid_trace11$count),  : 
  'from' must be a finite number
Calls: <Anonymous> ... continuous_scale -> check_breaks_labels -> seq -> seq.default

If you have any idea what could be causing this, I'd appreciate it. Thanks!!

[BaxW]

I've been trying to get to the bottom of this over the past few months, but I keep having the same issue described above. It looks like ChrBoard.html.nostructure.nolegacy.nomarkers.Rmd is failing at line 288 because my counts_hap1_file (diploid_gene_count_trace.hap1.txt) doesn't contain counts for all of the chromosomes, so everything is filtered out in line 145. The Rmd does knit for the chromosomes that are represented in diploid_gene_count_trace.hap1.txt, so I think this must be the heart of the issue.

I'm not sure why diploid_gene_count_trace.hap1.txt is missing chomosomes. I assume this happens because either do_count_hits_Hap() or print_hit_counts() is failing in some way during HaploDup. I say this because gmap seems to run correctly and gmap_hits_hap1.txt has all chromosomes represented. If you have any thoughts or advice about this I would really appreciate it. I can provide more detail or share the input files if need be. Thanks!

[BaxW]

@andreaminio is there a dataset I could use to test HaploDup to see if my data is the issue? I was thinking of using one of the assemblies from the HaploSync paper, but I can't find all the files I would need to run HaploDup when looking here. Is there somewhere else I should look?