ROOT file merge output problem

HI I’m a biologist. I’m trying to use CNVnator which relies on ROOT. When I qsub the job (SUN engine), something weird happens.

Below is my script:


#$ -pe single 12
#$ -V
#$ -cwd
#$ -o $HOME/sge_jobs_output/sge_job.$JOB_ID.out -j y
#$ -S /bin/bash
#$ -l mem_free=8G

cd $HOME/scratch/bwa/12878root/

/home/xug/CNVnator_v0.2.4/src/cnvnator -root NA12878_3.root -chrom 3 -merge /home/xug/scratch/bwa/*.root[/code]

Here I want to merge small .root files into NA12878_3.root for chromosome 3 But got errors like below:

Allocating memory ... Error in <TFile::TFile>: file NA12878_3.root does not exist Can't determine length for ''. No reference genome specified.

NA12878_3.root is the output I want to generate; but the error seems to indicate the file has existed, and computer is trying to search for that. This is so weird to me!

SO what’s the problem? thx


This errors seems to be linked either to how to use cnvnator and/or to how it is implemented. I recommend you contact the original authors of cnvnator for more detailed help.

One question … are you sure that the SUN engine worker nodes all have access to the directory $HOME/scratch?