equenza.extract error

[Xin Zheng]

hi all:

when I use equenza.extract function:

test <- sequenza.extract("NEW_PANEL_PAIR/SO1004-GW20T628C08_L3.seqz.gz", verbose = FALSE), I met the error  like this : MT 16170   A       4       16      4.0     1.0     0       hom     44      16      A       .       0' does not exist in current working directory ('/data/NGS/oss_nova_data_download.dinosaur/TEST') .

Anybody have a similar problem ?

[Duo Xie]

I have a similar problem:

Processing chr18:
Error: 'chr18    49470204    N    1    19    18.462    1.0    0    hom    58    13    N    .    0' does not exist in current working directory ('/data/xieduo/Immun_genomics/data/Łuksza_2022_Nature/results/5.sequenza').
Execution halted

And this I checked the data of chr18:

zcat /data/xieduo/Immun_genomics/data/Łuksza_2022_Nature/results/5.sequenza/PAAD43M5_bin50.seqz.gz|head -n 1
chromosome    position    base.ref    depth.normal    depth.tumor    depth.ratio    Af    Bf    zygosity.normal    GC.percent    good.reads    AB.normal    AB.tumor    tumor.strand

zcat /data/xieduo/Immun_genomics/data/Łuksza_2022_Nature/results/5.sequenza/PAAD43M5_bin50.seqz.gz|grep chr18
chr18    49470204    N    1    19    18.462    1.0    0    hom    58    13    N    .    0

​

Does anyone have some suggestions?

Best,

Duo

[supriya awasthi]

Hi all,

       I am also facing the same error after using seqzdata = sequenza.extract(data.file)

Error: 'chr1_KI270707v1_random    3905    N    3    17    5.667    1.0    0    hom    46    17    N    .    0' does not exist in current working directory

If anybody resolve such sort of issue please share

[satishkumar Ranganathan Ganakammal]

Hello ,

Did any one solve this issue ? if so please provide any insights on the same

Regards,

Satish

[YanLemon]

Hi all, 

I also encountered a similar problem when using it. I found through inspection that this problem may be related to the version of readr. By replacing read_tsv(file = paste(mstrsplit(x), collapse = "\n") in the three functions of read.seqz.chr() read.seqz.tbi() gc.sample.stats() with read_tsv(file = I(paste(mstrsplit(res), collapse = "\n"))) solved this error.

Hope it can help those in need

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