Error: unable to open

[dbhayal9]

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

[valeu]

Please add to the config (in [general]):

window = 30000

and run again?

[dbhayal9]

Hi @valeu Thanks for your reply, but getting same error

[valeu]

Dear user, do you understand which file FREEC attemps to open?

[valeu]

what files get created in the output directory?