Hi,
I'm getting the following error while running control freec:
Unable to open fasta file for chr Vې���,�7+�+o�����i���C-]HϧV@A���Z�r�A��h!�O�'XAX���'�������<M�٤���*F���|FX{�?�AI������h���a��[���x2�NM���G��3�cR��A�������Ҋ�� in folder /home/taha/Softwares/Human-Genome/hg19_chrs/humangenome19
Please note, /home/taha/Softwares/Human-Genome/hg19_chrs/humangenome19 should be a folder, not a file!
The input file i use is:
[general]
chrLenFile = hs19_1C.len
window = 3000
step = 1000
ploidy = 2
#breakPointThreshold = -.001
intercept=1
minMappabilityPerWindow = 0.7
outputDir = /media/Disk-2/Freec
sex=XY
breakPointType=4
#degree=3
#coefficientOfVariation = 0.05
gemMappabilityFile = /home/taha/Softwares/Gem/hg19/out76_hg19.gem
chrFiles = /home/taha/Softwares/Human-Genome/hg19_chrs/humangenome19/
[sample]
mateCopyNumberFile = /home/taha/Softwares/samtools-0.1.18/505C.sorted.bam
inputFormat = bam
mateOrientation = FR
[control]
mateCopyNumberFile = /home/taha/Softwares/samtools-0.1.18/505N.sorted.bam
inputFormat = bam
mateOrientation = FR
[BAF]
SNPfile = snp132.txt
minimalCoveragePerPosition = 5
[Target]
captureRegions = TargetSeq_exome_target_regions_hg19.bed
Can anybody help?
I'm getting the following error while running control freec:
Unable to open fasta file for chr Vې���,�7+�+o�����i���C-]HϧV@A���Z�r�A��h!�O�'XAX���'�������<M�٤���*F���|FX{�?�AI������h���a��[���x2�NM���G��3�cR��A�������Ҋ�� in folder /home/taha/Softwares/Human-Genome/hg19_chrs/humangenome19
Please note, /home/taha/Softwares/Human-Genome/hg19_chrs/humangenome19 should be a folder, not a file!
The input file i use is:
[general]
chrLenFile = hs19_1C.len
window = 3000
step = 1000
ploidy = 2
#breakPointThreshold = -.001
intercept=1
minMappabilityPerWindow = 0.7
outputDir = /media/Disk-2/Freec
sex=XY
breakPointType=4
#degree=3
#coefficientOfVariation = 0.05
gemMappabilityFile = /home/taha/Softwares/Gem/hg19/out76_hg19.gem
chrFiles = /home/taha/Softwares/Human-Genome/hg19_chrs/humangenome19/
[sample]
mateCopyNumberFile = /home/taha/Softwares/samtools-0.1.18/505C.sorted.bam
inputFormat = bam
mateOrientation = FR
[control]
mateCopyNumberFile = /home/taha/Softwares/samtools-0.1.18/505N.sorted.bam
inputFormat = bam
mateOrientation = FR
[BAF]
SNPfile = snp132.txt
minimalCoveragePerPosition = 5
[Target]
captureRegions = TargetSeq_exome_target_regions_hg19.bed
Can anybody help?