error in ngs.plot.r

[russell....@gmail.com]

Trying to conduct ngs.plot for ATACseq reads to create a TSS metaplot. Reaching the same error continuously, and wondering if it has to do with the UCSC genome used for alignment ("chr1" vs "1" etc.)

Command:

ngs.plot.r -G hg38 -R tss -C FTO-1_S17_R1_001.fastqtrim.bam.sorted.bam -O FTO-1.tss

Output/Error:

onfiguring variables...

Using database:

/software/ngsplot/database/hg38/hg38.ensembl.genebody.protein_coding.RData

Done

Loading R libraries.....Done

Analyze bam files and calculate coverageWarning messages:

1: 'BamSampler' is deprecated. Use 'REDUCEsampler' in the GenomicFiles package 

2: In headerIndexBam(bam.list) :

  Aligner for: FTO-1_S17_R1_001.fastqtrim.bam.sorted.bam cannot be determined. Style of 

standard SAM mapping score will be used.

Warning message:

'isNotPrimaryRead' is deprecated.

Use 'isSecondaryAlignment' instead.

See help("Deprecated") 

......................................................................Error in if (nrow(result.matrix) > 1 && se) { : 

  missing value where TRUE/FALSE needed

Execution halted