I have a problem to get sequenza.results - Error 'to'must be a finite number

[Lee jun yeop]

I tried to get sequenza.results but it is stopped with this error message

"Error in seq.default(0, max_coord_chr_i, by = 1e+07) :
  'to' must be a finite number"

This is my step.

In terminal

sequenza-utils bam2seqz -n normal.pe.st.rg.md.ab.bam -t tumor.pe.st.rg.md.ab.bam --fasta ucsc.hg19.fasta -gc ucsc.hg19.gc50Base.wig.gz -o tumor.seqz.gz

sequenza-utils seqz_binning --seqz tumor.seqz.gz -w 50 -o tumor.small.seqz.gz







and in R-studio


tumor <- sequenza.extract('tumor.small.seqz.gz')
tumorCP <- sequenza.fit(tumor)
sequenza.results(sequenza.extract = tumor, cp.table = tumorCP, sample.id = "tumor", out.dir = "tumor")

and error appeared

tumor <- sequenza.extract('tumor.small.seqz.gz')

Processing chrM:   15 variant calls.   1 copy-number segments.   0 heterozygous positions.   1110 homozygous positions.
Processing chr1:   2969 variant calls.   97 copy-number segments.   6429 heterozygous positions.   430672 homozygous positions.
Processing chr2:   2069 variant calls.   97 copy-number segments.   4743 heterozygous positions.   303109 homozygous positions.
Processing chr3:   1529 variant calls.   67 copy-number segments.   2905 heterozygous positions.   252859 homozygous positions.
Processing chr4:   1010 variant calls.   54 copy-number segments.   2423 heterozygous positions.   150110 homozygous positions.
Processing chr5:   1154 variant calls.   55 copy-number segments.   2676 heterozygous positions.   183562 homozygous positions.
Processing chr6:   1295 variant calls.   61 copy-number segments.   2438 heterozygous positions.   169400 homozygous positions.
Processing chr7:   1742 variant calls.   46 copy-number segments.   3570 heterozygous positions.   204259 homozygous positions.
Processing chr8:   1130 variant calls.   63 copy-number segments.   2108 heterozygous positions.   135941 homozygous positions.
Processing chr9:   1212 variant calls.   54 copy-number segments.   3051 heterozygous positions.   174133 homozygous positions.
Processing chr10:   1263 variant calls.   56 copy-number segments.   3231 heterozygous positions.   171989 homozygous positions.
Processing chr11:   1829 variant calls.   100 copy-number segments.   3402 heterozygous positions.   262506 homozygous positions.
Processing chr12:   1570 variant calls.   63 copy-number segments.   2863 heterozygous positions.   235706 homozygous positions.
Processing chr13:   520 variant calls.   18 copy-number segments.   1044 heterozygous positions.   70613 homozygous positions.
Processing chr14:   1032 variant calls.   46 copy-number segments.   1863 heterozygous positions.   142764 homozygous positions.
Processing chr15:   1056 variant calls.   26 copy-number segments.   2089 heterozygous positions.   155545 homozygous positions.
Processing chr16:   1364 variant calls.   47 copy-number segments.   3045 heterozygous positions.   187915 homozygous positions.
Processing chr17:   1828 variant calls.   73 copy-number segments.   3745 heterozygous positions.   263272 homozygous positions.
Processing chr18:   453 variant calls.   17 copy-number segments.   1299 heterozygous positions.   65232 homozygous positions.
Processing chr19:   2570 variant calls.   98 copy-number segments.   4099 heterozygous positions.   274655 homozygous positions.
Processing chr20:   734 variant calls.   27 copy-number segments.   1740 heterozygous positions.   111516 homozygous positions.
Processing chr21:   438 variant calls.   23 copy-number segments.   1192 heterozygous positions.   44826 homozygous positions.
Processing chr22:   1015 variant calls.   20 copy-number segments.   1639 heterozygous positions.   106967 homozygous positions.
Processing chrX:   538 variant calls.   7 copy-number segments.   914 heterozygous positions.   147443 homozygous positions.
Processing chrY:   13 variant calls.   6 copy-number segments.   550 heterozygous positions.   3595 homozygous positions.
Processing chr1_gl000191_random:   1 variant calls.   1 copy-number segments.   0 heterozygous positions.   19 homozygous positions.
Processing chr1_gl000192_random:

Error in data.frame(chrom, pos, wins.data, stringsAsFactors = FALSE) :   arguments imply differing number of rows: 13, 0

In addition: Warning message:In numericChrom(chrom) : NAs introduced by coercion
   3 variant calls.   1 copy-number segments.   13 heterozygous positions.   631 homozygous positions.
Processing chr4_ctg9_hap1:   2 variant calls.   1 copy-number segments.   0 heterozygous positions.   48 homozygous positions.
Processing chr4_gl000193_random:
Error in data.frame(chrom, pos, wins.data, stringsAsFactors = FALSE) :   arguments imply differing number of rows: 51, 0
In addition: Warning message:In numericChrom(chrom) : NAs introduced by coercion
   3 variant calls.   1 copy-number segments.   51 heterozygous positions.   365 homozygous positions.
Processing chr4_gl000194_random:
Error in data.frame(chrom, pos, wins.data, stringsAsFactors = FALSE) :   arguments imply differing number of rows: 40, 0
In addition: Warning message:In numericChrom(chrom) : NAs introduced by coercion
   7 variant calls.   1 copy-number segments.   40 heterozygous positions.   266 homozygous positions.
Processing chr6_apd_hap1:   1 variant calls.   1 copy-number segments.   0 heterozygous positions.   12 homozygous positions.
Processing chr6_cox_hap2:   6 variant calls.   1 copy-number segments.   0 heterozygous positions.   247 homozygous positions.
Processing chr6_dbb_hap3:   2 variant calls.   1 copy-number segments.   0 heterozygous positions.   99 homozygous positions.
Processing chr6_mann_hap4:   1 variant calls.   1 copy-number segments.   0 heterozygous positions.   78 homozygous positions.
Processing chr6_mcf_hap5:

Error in data.frame(chrom, pos, wins.data, stringsAsFactors = FALSE) :   arguments imply differing number of rows: 12, 0
In addition: Warning message:In numericChrom(chrom) : NAs introduced by coercion
   7 variant calls.   1 copy-number segments.   12 heterozygous positions.   304 homozygous positions.
Processing chr6_qbl_hap6:   2 variant calls.   1 copy-number segments.   0 heterozygous positions.   138 homozygous positions.
Processing chr6_ssto_hap7:
Error in data.frame(chrom, pos, wins.data, stringsAsFactors = FALSE) :   arguments imply differing number of rows: 1, 0
In addition: Warning message:In numericChrom(chrom) : NAs introduced by coercion
   2 variant calls.   1 copy-number segments.   1 heterozygous positions.   204 homozygous positions.
Processing chr7_gl000195_random:
Error in data.frame(chrom, pos, wins.data, stringsAsFactors = FALSE) :   arguments imply differing number of rows: 102, 0
In addition: Warning message:In numericChrom(chrom) : NAs introduced by coercion
   6 variant calls.   1 copy-number segments.   102 heterozygous positions.   339 homozygous positions.

tumorCP <- sequenza.fit(tumor)

 |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=05m 16s

sequenza.results(sequenza.extract = tumor, cp.table = tumorCP, sample.id = "tumor", out.dir = "tumor")

Error in seq.default(0, max_coord_chr_i, by = 1e+07) :
  'to' must be a finite number

After this, in directory, there are tumor_gc_plots.pdf, tumor_sequenza_extract.RData and unfinished tumor_chromosome_depths.pdf.

Could you teach me what is the problem? I guess problem from some errors during sequenza.extract or chr number setting, however I don't know how to fix it.

Thank you.