al2na
commented
7 years ago do you get the same error with destrand=TRUE?
On Wed, Mar 15, 2017 at 8:34 PM, Andrew Johnston notifications@github.com wrote:
Hi Akalin,
I'm getting the following error when uniting my sample with the following code:
meth<-unite(object = familyObj, destrand=TRUE, by=.EACHI, save.db = F)
Error in vecseq(f , len , if (allow.cartesian || notjoin || !anyDuplicated(f , : Join results in 216308346 rows; more than 60136491 = nrow(x)+nrow(i).
Check for duplicate key values in i each of which join to the same group in x over and over again. If that’s ok, try by=.EACHI to run j for each group to avoid the large allocation. If you are sure you wish to proceed, rerun with allow.cartesian=TRUE. Otherwise, please search for this error message in the FAQ, Wiki, Stack Overflow and datatable-help for advice.
I've checked to make sure that none of my samples have duplicate chr and coordinates using the following 1 liner $cut -f 2,3 ${dir}BSTag-Sample-${SampleName}-reprep_CpG.methylKit| sort | uniq -cd
I've also tried replicating the problem with only using 2-3 samples, but I received no error. I then tried to subset my 17 samples to just the first 1,000,000 lines; this received no error. I tried again when I used the first 5 million, and also received no error. I tried 10 million, and I got the same error (albeit less duplicates mentioned). I wanted to shrink the file sizes down so I subset the file to only rows>5,000,000 and less then 10,000,000; this returned the error:
Error in vecseq(f , len , if (allow.cartesian || notjoin || !anyDuplicated(f , : Join results in 11620518 rows; more than 7736026 = nrow(x)+nrow(i).
Check for duplicate key values in i each of which join to the same group in x over and over again. If that’s ok, try by=.EACHI to run j for each group to avoid the large allocation. If you are sure you wish to proceed, rerun with allow.cartesian=TRUE. Otherwise, please...
I tried to subset the files even further, such as 5,000,000 < rows < 7,500,000 and 7,500,000 < rows < 10,000,000, but this did not replicate the error. So unfortunately, I'm making available some large files which replicate the error.
The following is the code that I used (using the most recent github install of methylKit):
suppressPackageStartupMessages({ library(methylKit) }) library(RColorBrewer) library(gplots) library(knitr)
file.list=list("BS-TAG-Sample-77_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-78_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-79_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-80_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-81_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-82_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-83_CpG_percentFix_5000000.methylKit", "BSTag-Sample-84-reprep_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-85_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-86_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-87_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-88_CpG_percentFix_5000000.methylKit", "BSTag-Sample-89-reprep_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-90_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-91_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-92_CpG_percentFix_5000000.methylKit", "BS-TAG-Sample-93_CpG_percentFix_5000000.methylKit")
familyObj=methRead(file.list, sample.id=list("gm77", "gm78", "gm79", "gm80", "gm81", "gm82", "gm83", "gm84", "gm85", "gm86", "gm87", "gm88", "gm89", "gm90", "gm91","gm92", "gm93"), assembly="hg38_decoy_EBV", treatment=rep(0,17), context="CpG", mincov = 3)
meth_debug<-unite(object = familyObj, destrand=TRUE, by=.EACHI, save.db = F)
I've also tried
meth_debug<-unite(object = familyObj, destrand=TRUE)
I've placed the files in the following google drive (sorry about the size of the files): https://drive.google.com/drive/folders/0B1bAk0VjZmbVMURzOVJrWXVraUE? usp=sharing
Thank you for your help, Andrew
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/al2na/methylKit/issues/63, or mute the thread https://github.com/notifications/unsubscribe-auth/AAm9EbqAsKN-ctsib9cUPLCH9S_JdgHvks5rmD00gaJpZM4MebJy .
AJEinstein
KristenKrolick
alexg9010
Hi Akalin,
I'm getting the following error when uniting my sample with the following code:
I've checked to make sure that none of my samples have duplicate chr and coordinates using the following 1 liner
$cut -f 2,3 ${dir}BSTag-Sample-${SampleName}-reprep_CpG.methylKit| sort | uniq -cdI've also tried replicating the problem with only using 2-3 samples, but I received no error. I then tried to subset my 17 samples to just the first 1,000,000 lines; this received no error. I tried again when I used the first 5 million, and also received no error. I tried 10 million, and I got the same error (albeit less duplicates mentioned). I wanted to shrink the file sizes down so I subset the file to only rows>5,000,000 and less then 10,000,000; this returned the error:
I tried to subset the files even further, such as 5,000,000 < rows < 7,500,000 and 7,500,000 < rows < 10,000,000, but this did not replicate the error. So unfortunately, I'm making available some large files which replicate the error.
The following is the code that I used (using the most recent github install of methylKit):
I've placed the files in the following google drive (sorry about the size of the files): https://drive.google.com/drive/folders/0B1bAk0VjZmbVMURzOVJrWXVraUE?usp=sharing
Thank you for your help, Andrew