Off topic:GOplot error - Gene Ontology plot generation errors
0
0
Entering edit mode
Raito92 ▴ 60
@raito92-20399
Last seen 22 months ago
Italy

Hello, I'm trying to run the Trinity script prepnrunGOplot.pl to get plots after GO enrichment analysis (calculated with analyzediff_expr.pl), comparing two samples previously DE analyzed. It calls the goplot package, but I'm getting errors I can't understand

I ran:

./prep_n_run_GOplot.pl --GO_annots /home/genomica/DATA/Lattuga/go_annots.dat --DE_subset /home/genomica/DATA/Lattuga/edgeR_0.2/Matrici.gene.counts.matrix.DRR057333_48h_vs_DRR057083_48h.edgeR.DE_results.P0.001_C2.DE.subset --DE_GO_enriched /home/genomica/DATA/Lattuga/edgeR_0.2/Matrici.gene.counts.matrix.DRR057333_48h_vs_DRR057083_48h.edgeR.DE_results.P0.001_C2.DE.subset.GOseq.enriched --tmpdir /home/genomica/DATA/Lattuga/GOPLOT --pdf_filename GOPLOT_48LL_VS_48LD

And got this:

WARNING, no GO term info found for: GO:0044763, skipping...
    WARNING, no GO term info found for: GO:0044710, skipping...
    WARNING, no GO term info found for: GO:0051183, skipping...
    WARNING, no GO term info found for: GO:0044711, skipping...
    CMD: /mnt/d8e73111-db5e-4011-87aa-e4d64fb8c1e9/DATA/Software/Trinity/trinityrnaseq-2.8.5/Analysis/DifferentialExpression/GOplot.Rscript --EC_david /home/genomica/DATA/Lattuga/GOPLOT/EC.david --EC_genelist /home/genomica/DATA/Lattuga/GOPLOT/EC.genelist --pdf_outfile GOPLOT_48LL_VS_48LD
    Carico il pacchetto richiesto: ggplot2
    Carico il pacchetto richiesto: ggdendro
    Carico il pacchetto richiesto: gridExtra
    Carico il pacchetto richiesto: RColorBrewer
    Generating plot pdf file: GOPLOT_48LL_VS_48LD
    GOBar, circ, BP
    GOBar, circ, multiple
    GOBar, multiple, Z-scores
    GOBubble, multiple
    Warning message:
    Removed 115 rows containing missing values (geom_point).
    GOBubble, bckgrd color
    Warning message:
    Removed 115 rows containing missing values (geom_point).
    GOCircle
    Error in f(..., self = self) : Breaks and labels are different lengths
    Calls: GOCircle ... guide_train -> guide_train.colorbar -> <Anonymous> -> f
    Inoltre: Warning messages:
    1: Removed 5 rows containing missing values (geom_point).
    2: Removed 5 rows containing missing values (geom_point).
    Esecuzione interrotta
    Error, CMD: /mnt/d8e73111-db5e-4011-87aa-e4d64fb8c1e9/DATA/Software/Trinity/trinityrnaseq-2

Can anyone help me here? Thanks in advance. What could be wrong in my input files?

goplot gene ontology • 333 views
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 597 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6