Root File Output Problem

Question

[Bioscientist]

Hi I'm trying to use CNVnator which relies on ROOT. When I qsub the job, something weird happen.

Below is my script:

#!/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

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

[brentp]

have you tried adding -chrom 1 2 3 ... For each of your *.root files?

[Bioscientist]

sorry, i don't quite get your point. but each *.root file contains the information for all chromosomes.......thx

[Jeremy Leipzig]

does this problem only occur with qsub? what happens when you run it yourself?

Answer 1

[Istvan Albert]

Error messages can be misleading and some detective work is often necessary. It could be that the output file generation is a multistage process, it first creates the file, then it modifies it at a later step. If your process skips the first stage for some reason and tries the second and would lead to the error you see.

So don't get too hung up on the exact wording.

In this particular case I would focus on the second message which may indicate that one of the files you are trying to merge may be in an incorrect format.

[Hranjeev]

@Itsvan Albert this is a test

[Hranjeev]

@bioscientist test two