Error with sequenza.extract function

[Hima Anbunathan]

Hi Francesco,

I am getting the following error with sequenza.extract function:

test <- sequenza.extract(data.file)

Processing chr22: 1 variant calls; 633 heterozygous positions; 839754 homozygous positions.

Processing chrX: 3 variant calls; 678 heterozygous positions; 1248868 homozygous positions.

Processing chrY: 1 variant calls; 179 heterozygous positions; 102898 homozygous positions.

Processing chrM: Error in data.frame(chrom, pos, wins.data, stringsAsFactors = FALSE) : 

  arguments imply differing number of rows: 9, 0

In addition: Warning message:

In numericChrom(chrom) : NAs introduced by coercion

Error in if (!is.null(breaks) & nrow(breaks) > 0) { : 

  argument is of length zero

I checked the input files, but it does not seem there is anything wrong with it:

head file1.seqz 

chromosome position base.ref depth.normal depth.tumor depth.ratio Af Bf zygosity.normal GC.percent good.reads AB.normal AB.tumor tumor.strand

chr1 13183 A 8 12 1.5 1.0 0 hom 56.0 1 A . 0

chr1 13184 G 8 12 1.5 1.0 0 hom 56.0 1 G . 0

chr1 13185 C 9 12 1.333 1.0 0 hom 56.0 1 C . 0

tail file1.seqz 

chrM 16557 T 31 17 0.548 1.0 0 hom 33.3333333333 1 T . 0

chrM 16558 A 33 17 0.515 1.0 0 hom 33.3333333333 1 A . 0

chrM 16559 A 33 17 0.515 1.0 0 hom 33.3333333333 1 A . 0

zcat file1.pileup.gz | cut -f 1 | uniq

chr1

chr2

chr3

chr4

chr5

chr6

chr7

chr8

chr9

chr10

chr11

chr12

chr13

chr14

chr15

chr16

chr17

chr18

chr19

chr20

chr21

chr22

chrX

chrY

chrM

zcat file1.seqz.gz | cut -f 1 | uniq

chromosome

chr1

chr2

chr3

chr4

chr5

chr6

chr7

chr8

chr9

chr10

chr11

chr12

chr13

chr14

chr15

chr16

chr17

chr18

chr19

chr20

chr21

chr22

chrX

chrY

chrM

Would you happen to know why this is so?

Thanks,

Hima

[Francesco Favero]

Dear Hima,

Unfortunately chromosome M gives problems in the extraction step. Probably because of the lack of heterozygous positions.

I should implement a cleaner way to handle this situation in future versions.

Could you try to select the chromosomes to sequenza.extract in the argument "chromosome.list"? You can pass a vector of the chromosome you would like to extract, eg: paste0(" chr", c(1:22,"X","Y").

Best

Francesco

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[彭国禹]

Hello Francesco, my problem is `seqz` file contains only `chrM`. My cmd like:

```

md = ['sequenza-utils', 'bam2seqz', '-n', p1_bam, '-t', input_path, '--fasta', hg19_fa, '-gc', hg19_gc_wig, '-o', output_path]
```

I want to what may the reason. Thnaks.
在 2015年12月8日星期二 UTC+8上午5:56:38，Francesco Favero写道：

Dear Hima,

Unfortunately chromosome M gives problems in the extraction step. Probably because of the lack of heterozygous positions.

I should implement a cleaner way to handle this situation in future versions.

Could you try to select the chromosomes to sequenza.extract in the argument "chromosome.list"? You can pass a vector of the chromosome you would like to extract, eg: paste0(" chr", c(1:22,"X","Y").

Best

Francesco

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[Francesco Favero]

Hi,

Can you check that your GC file and the bam files you are using have the same chromosome order?

If not you may use a chromosome per chromosome approach.

Best

Francesco

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