Rscript $scriptsdir/hap_analysis.r -v BnaA03G0131100ZS.recode.vcf -g $datadir/ZS11.v0.gff3 -p $datadir/huaqi2025.txt -G $datadir/group.txt -c scaffoldA01 -s 6643999 -e 6644632

WARNING: ignoring environment value of R_HOME

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Registered S3 method overwritten by 'pegas':

  method      from    

  [.haplotype genetics

Attaching package: ‘geneHapR’

The following objects are masked _by_ ‘.GlobalEnv’:

    gff, pheno, vcf

Scanning file to determine attributes.

File attributes:

  meta lines: 3381

  header_line: 3382

  variant count: 16

  column count: 279

Meta line 3381 read in.

All meta lines processed.

gt matrix initialized.

Character matrix gt created.

  Character matrix gt rows: 16

  Character matrix gt cols: 279

  skip: 0

  nrows: 16

  row_num: 0

Processed variant: 16

All variants processed

Extracting gt element GT

Warning message:

Removed 1 rows containing missing values (`geom_text()`). 

null device 

          1 

Error in if (strand == "+") mapLabel <- paste0(mapLabel, "\n5' -> 3'") else mapLabel <- paste0(mapLabel,  : 

  missing value where TRUE/FALSE needed

Calls: plot_LDheatmap -> LDheatmap -> LDheatmapMapNew.add

Execution halted