Question: How to run EXCAVATOR2?
0
gravatar for pradyumna Sagar
3 months ago by
Manipal, School Of Life Sciences
pradyumna Sagar20 wrote:

I have downloaded and installed all the dependencies for excavator2 tool, I have created the target, and while creating data prepare step I ran the following command perl EXCAVATORDataPrepare.pl melas_prepare.txt --processors 6 --target melas20k --assembly hg19

I got the following error:

Working on sample M1.
Creating Read Count Data...
Removing temporary files...
Read Count done!
Normalizing Read Count Data...
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2
Attaching package: ‘Hmisc’
The following objects are masked from ‘package:base’:
format.pval, round.POSIXt, trunc.POSIXt, units
Error in quantile.default(RCTL[ind], c(0.1, 0.9)) : 
missing values and NaN's not allowed if 'na.rm' is FALSE
Calls: QuantileLength -> rbind -> quantile -> quantile.default
Execution halted

How to resolve the issuel?

excavator2 R • 225 views
ADD COMMENTlink modified 11 weeks ago • written 3 months ago by pradyumna Sagar20
1
gravatar for Kevin Blighe
12 weeks ago by
Kevin Blighe9.3k
London
Kevin Blighe9.3k wrote:

Hey, it looks like the problem is that you have missing values in your dataset. These are not permitted. If you remove all samples with missing values, then it may run correctly.

ADD COMMENTlink written 12 weeks ago by Kevin Blighe9.3k
1

Hi, I just found out that the issue was with the R script in package and the R version I am using. The problem was resolved by changing na.rm value from na.rm=T to na.rm=TRUE in all the scripts.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by pradyumna Sagar20

A type of error that I've not seen before! Luckily, by default, I always write TRUE or FALSE and never T or F.

ADD REPLYlink written 11 weeks ago by Kevin Blighe9.3k
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