SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
ONCOCNV: a method to extract CNAs from amplicon (or targeted) sequencing data valeu Bioinformatics 13 02-24-2018 02:03 AM
tophat running error figo1019 Bioinformatics 9 05-03-2013 08:18 AM
TopHat error - error running prep_reads ajaffe RNA Sequencing 0 11-29-2012 08:09 AM
tophat Error running running 'prep_reads' victoryhe Bioinformatics 2 10-17-2011 05:53 AM

Reply
 
Thread Tools
Old 12-05-2019, 01:52 PM   #1
mwarrier
Junior Member
 
Location: usa

Join Date: Dec 2019
Posts: 1
Default Error in mvnX when running processSamples.R of OncoCNV

Hi,

I tried to run ONCOCNV.sh (most recent version) on a set of 9 normal sample alignments to generate a baseline to call CNVs on a set of 8 tumor samples. I used an appropriate tab-delimited BED file (chr, start, end, amplicon ID, 0, and gene name), BAM alignments, and an Ensembl reference genome. All tool requirements were satisfied. However, I was getting the following error with processSamples.R:

running processSamples.R
Package 'mclust' version 5.4.5
Type 'citation("mclust")' for citing this R package in publications.
PSCBS v0.65.0 successfully loaded. See ?PSCBS for help.

Attaching package: ‘PSCBS’

The following objects are masked from ‘package:base’:

append, load
R.cache v0.13.0 (2018-01-03) successfully loaded. See ?R.cache for help.
Loading required package: lattice
Loading required package: grid
Loading required package: parallel
Error in mvnX(data = data, prior = prior) :
NA/NaN/Inf in foreign function call (arg 1)
Calls: predictClust ... eval -> eval -> mclustBIC -> mvn -> eval -> eval -> mvnX
In addition: Warning messages:
1: In chrom != "chrM" & chrom != "chrX" & chrom != "chrY" & chrom != :
longer object length is not a multiple of shorter object length
2: In chrom != "chrM" & chrom != "chrX" & chrom != "chrY" & chrom != :
longer object length is not a multiple of shorter object length
3: In chrom != "chrM" & chrom != "chrX" & chrom != "chrY" & chrom != :
longer object length is not a multiple of shorter object length
4: In rnorm(length(autoInd), 0, sdError[autoInd]) : NAs produced
Execution halted

I want to mention that the Control.stats.Processed.txt file from processControls.R contained some fields with missing values (NA) for mean and IC1-3. Replacing those values with arbitrary numbers did not seem to help. Any clues as to what could be causing this error would be much appreciated.

Thank you!
mwarrier is offline   Reply With Quote
Reply

Tags
bioinformatics, cnv variant calling, oncocnv

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:22 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO