Help with CNA analysis using control-FREEC

Question

[sainavyav22]

Hello,

I am working whole genome illumina sequenced data of dog tumor and matched normal DNA. I wanted to perform CNA analysis, I am using control-FREEC software for this purpose. I received an error message saying the FREEC is not able to read the input file. I attached the script I used. Could someone please help me with this? Thanks.

Error message: FREEC was not able to extract reads from /projects/2348_Tumor_alignment_sorted.bam
Check your parameters: inputFormat and mateOrientation
Use "matesOrientation=0"

Configutaion file: (These are paired-end-sequenced reads)

[general]
chrLenFile = /projects/canFam3.chrom.sizes.txt
ploidy = 2
breakPointThreshold = 0.8
window = 50000
minExpectedGC = 0.3
maxExpectedGC = 0.5
chrFiles = Dog_Genome_Chromosomes
outputDir = /projects/freec_2348

[sample]
mateFile = /projects/2348_Tumor_alignment_sorted.bam
inputFormat = BAM
mateOrientation = FR

[control]
mateFile = /projects/2348_Genome_alignment_sorted.bam
inputFormat = BAM
mateOrientation = FR

Command used to run:

./freec -conf 2348_Tumor_ContigFile.txt

[Pierre Lindenbaum]

what is the output of the following commands:

ls -la /projects/2348_Genome_alignment_sorted.bam
ls -la ./projects/2348_Genome_alignment_sorted.bam

[sainavyav22]

Hi thanks for the reply. The output of both of the commands is same. Here you go!

-rw-rw-r-- 1 sainavyav22 arc.lymphoma_data 46637618653 Mar 17 19:35 2348_Genome_alignments_sorted.bam

[Pierre Lindenbaum]

so you're running this command from the root folder ?

[sainavyav22]

Yes! I specified the path to all the input files in my configuration file. Is there anything wrong in that?