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shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases
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Maize genome issues #97

Open Raoyugithub opened 2 years ago

Raoyugithub commented 2 years ago

Hi, I have installed the maize genomes, but Ig ot the following error code while while the script:

ngs.plot.r -G  B73    -R genebody  -C  ../9_rep1_rmp.bam    -O Kla_gene  -T  Arabi_4ac  -L 300 -FL 300
Configuring variables...
Using database:
/public/home/qtxu/software/ngsplot/NGSPLOT/ngsplot/database/B73/B73.ensembl.genebody.protein_coding.RData
Done
Loading R libraries.....Done
Analyze bam files and calculate coverageWarning message:
'isNotPrimaryRead' is deprecated.
Use 'isSecondaryAlignment' instead.
See help("Deprecated") 
.Done
Plotting figures...Error in plotheat(reg.list, uniq.reg, enrichList, v.low.cutoff, go.algo,  : 
  object 'g.order' not found
Execution halted

I have checked the genomes, it showed that the genome was sucessfully installed. 

ngsplotdb.py list
ID       Assembly                 Species              EnsVer   NPVer    InstalledFeatures            
AGPv3    AGPv3                    zea_mays             21.0     3.0      exon,genebody,tss,tes        
B73      Zm-B73-REFERENCE-NAM-5.0 zea_mays             53.0     3.0      exon,genebody,tss,tes        
hg19     GRCh37                   homo_sapiens         75.0     3.0      cgi,exon,genebody,tss,tes    
MSUv7    MSUv7                    oryza_sativa         0.0      3.0      exon,genebody,tss,tes        
Rapdb    IRGSP-1.0                oryza_sativa         52.0     3.0      exon,genebody,tss,tes        
Tair10   TAIR10                   arabidopsis_thaliana 21.0     3.0      exon,genebody,tss,tes

What had went wrong? Could any one help me out? Thanks!!!