Sequneza Error using Whole genome sequencing data

Question

[himyplans]

Hi,

I got an sequneza error using whole genome seqeuncing

In R,

test = sequenza.extract(data.file, verbose=FALSE, assembly="hg19")

Error messages:

Warning: 8 parsing failures.

row col expected actual file

1 position an integer position '12TB.seqz.gz'

1 depth.normal an integer depth.normal '12TB.seqz.gz'

1 depth.tumor an integer depth.tumor '12TB.seqz.gz'

1 depth.ratio a double depth.ratio '12TB.seqz.gz'

1 Af a double Af '12TB.seqz.gz' ... ............ .......... ............ ...................

See problems(...) for more details.

Error in seq.int(range.pos[1], range.pos[2], by = window.offset) :

'to' must be a finite number

In addition: Warning messages:

1: In read_tokens_(data, tokenizer, col_specs, col_names, locale_, :

NAs introduced by coercion to integer range

2: In min(x) : no non-missing arguments to min; returning Inf

Please let me know how to fix this error.

Thank you.