Error: unable to open #155
Description
Hi Team,
Please have a look i am unable to run FREEC-11.6.
Thanks in advance
my config file
###For more options see: http://boevalab.com/FREEC/tutorial.html#CONFIG ###
[general]
chrLenFile = /home/ubuntu/Doc/CNVSOM/FREEC-11.6/input/Homo_sapiens_assembly38cleaned.fasta.fai
#window = 0
ploidy = 2
outputDir = /home/ubuntu/Doc/CNVSOM/FREEC-11.6/confreeresult
#sex=XY
breakPointType=4
chrFiles = /home/ubuntu/Doc/nf/hg381_22XYM/
maxThreads=30
breakPointThreshold=1.2
noisyData=TRUE
printNA=FALSE
readCountThreshold=50
[sample]
mateFile = /home/ubuntu/Doc/CNVSOM/cnv_results/4.MarkDuplicates/SRR645579_sorted_md.bam
inputFormat = BAM
mateOrientation = 0
[control]
mateFile =
inputFormat = BAM
mateOrientation =
[BAF]
#SNPfile = /bioinfo/users/vboeva/Desktop/annotations/hg19_snp131.SingleDiNucl.1based.txt
#minimalCoveragePerPosition = 5
[target]
#captureRegions = /EXOME-SEQ/TruSeq_exome_targeted_regions.hg19.bed
Error
./freec -conf ../data/config_exome.txt
Control-FREEC v11.6 : a method for automatic detection of copy number alterations, subclones and for accurate estimation of contamination and main ploidy using deep-sequencing data
Multi-threading mode using 30 threads
..Breakpoint threshold for segmentation of copy number profiles is 1.2
..telocenromeric set to 50000
..FREEC is not going to output normalized copy number profiles into a BedGraph file (for example, for visualization in the UCSC GB). Use "[general] BedGraphOutput=TRUE" if you want a BedGraph file
..FREEC is not going to adjust profiles for a possible contamination by normal cells
Warning: 'coefficientOfVariation' or 'window' must be provided
..FREEC will use the coefficientOfVariation=0.05 to evaluate window size
..Output directory: /home/ubuntu/Doc/CNVSOM/FREEC-11.6/confreeresult
..Directory with files containing chromosome sequences: /home/ubuntu/Doc/nf/hg381_22XYM/
..Sample file: /home/ubuntu/Doc/CNVSOM/cnv_results/4.MarkDuplicates/SRR645579_sorted_md.bam
..Sample input format: BAM
..will use this instance of samtools: 'samtools' to read BAM files
..Control file:
..Input format for the control file: BAM
..Polynomial degree for "Sample ReadCount ~ Control ReadCount" normalization is 1
..Minimal CNA length (in windows) is 1
..File with chromosome lengths: /home/ubuntu/Doc/CNVSOM/FREEC-11.6/input/Homo_sapiens_assembly38cleaned.fasta.fai
..uniqueMatch = FALSE
..average ploidy set to 2
..break-point type set to 4
Warning: Parameter '[general] noisyData=true' will not have effect since FREEC won't use BAF information to correct predicted copy numbers
..minimal number of reads per window in the control sample is set to 50
..Control-FREEC will not look for subclones
..File /home/ubuntu/Doc/CNVSOM/FREEC-11.6/input/Homo_sapiens_assembly38cleaned.fasta.fai was read
total genome size: 3.08827e+09
..samtools should be installed to be able to read BAM files
read number: 43910657
coefficientOfVariation: 0.05
evaluated window size: 28132
..[genomecopynumber] Starting reading /home/ubuntu/Doc/CNVSOM/cnv_results/4.MarkDuplicates/SRR645579_sorted_md.bam
..samtools should be installed to be able to read BAM files; will use the following command for samtools: samtools view -@ 30 /home/ubuntu/Doc/CNVSOM/cnv_results/4.MarkDuplicates/SRR645579_sorted_md.bam
..finished reading /home/ubuntu/Doc/CNVSOM/cnv_results/4.MarkDuplicates/SRR645579_sorted_md.bam
PROFILING [tid=140108955424576]: /home/ubuntu/Doc/CNVSOM/cnv_results/4.MarkDuplicates/SRR645579_sorted_md.bam read in 34 seconds [fillMyHash]
43910657 lines read..
43899328 reads used to compute copy number profile
printing counts into /home/ubuntu/Doc/CNVSOM/FREEC-11.6/confreeresult/SRR645579_sorted_md.bam_sample.cpn
..Window size: 28132
..File /home/ubuntu/Doc/CNVSOM/FREEC-11.6/input/Homo_sapiens_assembly38cleaned.fasta.fai was read
..[genomecopynumber] Starting reading
Error: unable to open