How to run EXCAVATOR2?

Question

[pradyumna Jayaram]

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?

Answer 1

[Kevin Blighe]

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.

[pradyumna Jayaram]

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.

[Kevin Blighe]

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

[aykaz.eremyan]

Where exactly did you change the value? I'm getting a very similar error, but I'm not running any R scripts.

[pradyumna Jayaram]

Even I didn't run any R script myself, those scripts are run by perl wrapper, there are some R scripts in the folder. If you are getting the exact same error then change the value. or else update your R version and check back. It would be helpful if you provide the error message you are getting.

[Kevin Blighe]

What is the error and what code are you running?

[aykaz.eremyan]

I am running EXCAVATORDtatPrepare.pl as a part of my pipeline.

EXCAVATORDataPrepare.pl D3232 --processors 8 --target SureSelect7_10K --assembly hg19 --verbose

I am getting a repeating error:

[E::hts_open_format] Failed to open file NA
samtools view: failed to open "NA" for reading: No such file or directory
Error in seq.default(2, length(tt) * 2, by = 2) :
  wrong sign in 'by' argument
Calls: seq -> seq.default
Execution halted

[Kevin Blighe]

Check for simple things like your contig names matching to the contigs of the hg19 assembly that EXCAVATAOR is using. Also check that you have all dependencies installed. For example, the perl script clearly calls SAMtools - do you have a global SAMtools installed?

What is D3232? Where is it located?