cnaclinic's People
Forkers
haoziyeung frogman141 miro1942 linhxxx flywind2 nrlab-cruk masoodzaka d-fernandez-garcia ssyang145 ivicts dshcherbo qiangfu-eu novapyth mdugo vyellapa sharvarimankamecnaclinic's Issues
R_Realloc' could not re-allocate memory
Hello,
I am trying to use CNAclinic for CNV calling in a cfDNA WGS data with high coverage around 100x which leads to a ~200 GBs bam file. However, running CNAclinic at the first step when using the processForSegmentation() function face error due to the memory allocation on the cluster which can not be solved even by allocating 200 GB of memory.
I noticed this error can be solved by chunkSize in QDNAseq tool. So, I wonder if there is any option like that in CNAclinic to optimize the bin segmentation process?
Thanks in advance.
The error i got:
IH01-simulated-s1_sorted (1 of 1): extracting reads ...Error in value[3L] :
'R_Realloc' could not re-allocate memory (18446744065128005632 bytes)
file: /work/FAC/FBM/DBC/cdessim2/default/fpalizba/cfDNA-CNV/validation/IH01-simulated/IH01-simulated-s1_sorted.bam
index: NA
Calls: processForSegmentation ... tryCatch -> tryCatchList -> tryCatchOne ->
Execution halted
runsegmentation error
Hi,
I am getting the following error with runSegmentation on R v4.0.2:
The following error occured in HMMcopy::HMMsegment() Error: RangedData objects are defunct. Please migrate your code to use GRanges or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData
The HMM algorithm will be skipped
Error in runSegmentation(processedData, genome = "hg19") : HMMcopy segmentation did not return the expected number of bins or samples
Will there be an update to resolve the defunct objects?
Thanks,
Paul
runSegmentation (.reorderbyChrom) error
.reorderbyChrom function in runSegmentation results in " In xtfrm.data.frame(x) : cannot xtfrm data frames" error due to original code ( x <- x[order(x["chromosome"], x["start"]), ] ) being unable to successfully arrange chromosomes in ascending order.
Please consider updating to: x <- dplyr::arrange(x,chromosome)
Any plan to make an exome analysis ?
Error: 'RangedData' is not an exported object from 'namespace:IRanges'
Hi, i'm trying to run the example of segmentation in R version 4.1.3:
data(exData)
exData <- exData[exData$chromosome == "1", ]
CNAData <- runSegmentation(exData, genome="hg19",
segmentType=c("CBS", "PLS", "HMM"),
segmentsToSummarise=c("CBS", "PLS", "HMM"),
summaryMethod="mean")
But i get the following error:
Running HMMcopy segmentation
P16_SF_Bx
The following error occured in HMMcopy::HMMsegment()
Error: 'RangedData' is not an exported object from 'namespace:IRanges'
The HMM algorithm will be skipped
Error in runSegmentation(exData, genome = "hg19", segmentType = c("CBS", :
HMMcopy segmentation did not return the expected
number of bins or samples
In addition: Warning messages:
1: In xtfrm.data.frame(x) : cannot xtfrm data frames
2: In xtfrm.data.frame(x) : cannot xtfrm data frames
The same error happens when running with the output of processForSegmentation
Thank you very much
hg38 data
Hello,
I'd like to run my data on hg38 through your really cool-looking pipeline; however I only see hg19 mentioned in processforSegmentations. Is it possible to use data from hg38?
Thanks
Error in if (class(medianReadsPerBin) == "numeric") { : the condition has length > 1
Hi,
I am running the function optimalBinsize on a bunch of shallow WGS .bam files in R version 4.2.1
When the last sample is processed by the function, I get the following error:
Error in if (class(medianReadsPerBin) == "numeric") { : the condition has length > 1
The problem is that when multiple bam files are processed class(medianReadsPerBin)
outputs "matrix" "array"
causing the condition to have length > 1.
Best
Is CNAclinic also suitable for WES data?
I was wondering if this very great pipeline of analysis can be also adapted on Whole Exome Sequencing data, did you already performed any test?
Thank you!
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. ๐๐๐
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google โค๏ธ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.