ROOT file merge output problem

ROOT
1

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:

[code]#!/bin/bash

#$ -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

2

Hi,

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?

Philippe.