File uploading about maftools

[PoisonAlien]

Hi,

Its hard to say without a reproducible example. Can your share your file if you're okay with it ? or can you try to read using data.table::fread(maf_file) and see if you get the same error ? Is the file same as yesterday, error says file might be empty. Can you check the contents ?

[zayni]

Error in data.table::fread(coad.maf) :
Input is either empty or fully whitespace after the skip or autostart. Run again with verbose=TRUE.
I looked at the file. It is fine. Same as yesterday TCGA..COAD mutect file

Thanks a lot!
zayni

[PoisonAlien]

Is it compressed ? If so, can you decompress and try again ? Can you upload it here ?

[zayni]

It is not compressed at all. It is larger than 10MB. But it has all 32 fields of TCGA file
Thanks for your time

Zayni

[zayni]

Here is the link

https://portal.gdc.cancer.gov/files/706d5716-be1e-4482-a867-61dec69557c8

[PoisonAlien]

Hi,

Just downloaded the file and checked on macOS (Sierra) and Ubuntu, works fine for me.

coad = read.maf(maf = '~/Downloads/gdc_download_20170410_034802/706d5716-be1e-4482-a867-61dec69557c8/TCGA.COAD.mutect.706d5716-be1e-4482-a867-61dec69557c8.somatic.maf.gz')

can you post your command ?

[zayni]

library("maftools")

suppressPackageStartupMessages(require(maftools))
coad.maf = system.file(maf ='~/Downloads/gdc_download_20170410_034802/706d5716-be1e-4482-a867-61dec69557c8/TCGA.COAD.mutect.706d5716-be1e-4482-a867-61dec69557c8.somatic.maf.gz', package = 'maftools')
coad = read.maf(maf = laml.maf, removeSilent = TRUE, useAll = FALSE)
Error in is.data.frame(x = maf) : object 'laml.maf' not found
coad = read.maf(maf = coad.maf, removeSilent = TRUE, useAll = FALSE)
reading maf..
Error in data.table::fread(input = maf, sep = "\t", stringsAsFactors = FALSE, :
Input is either empty or fully whitespace after the skip or autostart. Run again with verbose=TRUE.

[zayni]

Thanks a lot !

[PoisonAlien]

Okay! you don't have to run first line system.file, since it points to example maf file which comes with the package. For your coad maf, you just need to provide downloaded file name (with path) to read.maf.

Try this:

coad = read.maf(maf = '~/Downloads/gdc_download_20170410_034802/706d5716-be1e-4482-a867-61dec69557c8/TCGA.COAD.mutect.706d5716-be1e-4482-a867-61dec69557c8.somatic.maf.gz', removeSilent = TRUE, useAll = FALSE)

[zayni]

Awesome ! It worked. Thanks you so much

[PoisonAlien]

No problem :)