running Control-FREEC on multiple tumor/normal paired samples

[awast]

Hi,
I am using this tool to identify cnvs from wes data . I have 30 tumor/matched normal paired samples. As i am able to run this tool on individual tumor-normal paired samples using config.txt . I want to run on all samples together is there any way to mention all tumor and all normal files together instead of running config.txt for every sample one by one.
I have tried to run this in way

1. cat listfile | while read i ; do $path/FREEC-11.6/src/./freec -conf $path/config_exome.txt -sample $path/"$i"_T_recal_reads.bam -control $path/"$i"_N_recal_reads.bam ; done.
   after implementing above command it is only consider tumor samples but not the matched normal and i am getting this :
   You did not provide a control sample ('mateFile' or 'mateCopyNumberFile') but you are working with targeted sequencing data that has a capture bias.****

my config file format is like:
[general]
chrLenFile =$path/data/hg38.fa.fai
window = 0
ploidy = 2,3,4
outputDir = $path/freec_results
#sex=XY
breakPointType=4
chrFiles = /mnt/raid1/somatic_copy_number_variation_analysis/FREEC-11.6/data/genome-file-chr
maxThreads=40

breakPointThreshold=1.2
noisyData=TRUE
printNA=FALSE
sambamba = $path/bin/./sambamba
readCountThreshold=50

[sample]

#mateFile = $path/CaGB_1_T_recal_reads.bam
inputFormat = BAM
mateOrientation = FR

[control]

#mateFile = $path/CaGB_1_N_recal_reads.bam
inputFormat = BAM
mateOrientation = FR

[BAF]

SNPfile = $path/dbSNP155.hg38.vcf.gz
minimalCoveragePerPosition = 5

[target]

#captureRegions = /EXOME-SEQ/TruSeq_exome_targeted_regions.hg19.bed
captureRegions = $path/final-file-sorted.bed
Please suggest a way to run on multiple tumor and matched normal together .

[valeu]

Thank you for sharing the error. What happens if you run FREEC for just one sample and one control? Do you also get a message that the control file is not found?

[awast]

Hi Mam,
Thankyou for the prompt reply. With reference to only one sample and one control, FREEC is running well and even not showing any message.

[valeu]

Then I guess you need to debug your bash loop... Maybe printing out the names of files and manually checking that everything is correct might help.