Error: unable to open file or unable to determine types for file

[stroke1989]

Hi,
I'm a new to FREEC. Thanks for this excellent tool. I tired to use FREEC to analyze CNV + LOH of my WES data. However, ERROR occurred:
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 6 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
..Window = 0 was set
..Output directory: /home/ug0416/software/FREEC-11.6/data/output
..Directory with files containing chromosome sequences: /home/ug0416/ref_hg19/ucsc_hg19_chromosome
..will use a threshold of 5 read(s) per SNP position to calculate beta allel frequency (BAF) values
..Sample file: /home/ug0416/mydata/05.gatk/a.BQSR/2nd_BQSR/SCA_082_T.sorted.markdup.recal.bam
..Sample input format: BAM
..will use this instance of samtools: '/home/ug0416/.conda/envs/sambamba/bin/samtools' to read BAM files
..Control file: /home/ug0416/mydata/05.gatk/a.BQSR/2nd_BQSR/SCA_082_N.sorted.markdup.recal.bam
..Input format for the control file: BAM
FREEC will create a pileup to compute BAF profile!
...File with SNPs : /home/ug0416/software/FREEC-11.6/data/hg19_snp142.SingleDiNucl.1based.bed
..forceGCcontentNormalization was set to 1: will use GC-content to normalize the read count data
..minimal expected GC-content (general parameter "minExpectedGC") was set to 0.35
..maximal expected GC-content (general parameter "maxExpectedGC") was set to 0.55
..Minimal CNA length (in windows) is 3
..File with chromosome lengths: /home/ug0416/software/FREEC-11.6/data/hg19.len
..File /home/ug0416/software/FREEC-11.6/data/hg19.len was read
..Using the default minimal mappability value of 0.85
..uniqueMatch = FALSE
..FREEC will try to guess the correct ploidy (for each ploidy specified in 'ploidy' parameter)
..It will try ploidies: 2
3
..break-point type set to 4
..noisyData set to 1
..minimal number of reads per window in the control sample is set to 60
..Control-FREEC will not look for subclones
Creating Pileup file to compute BAF profile...
..will increase flanking regions by -1252 bp
Error: unable to open file or unable to determine types for file /home/ug0416/software/FREEC-11.6/data/output/SCA_082_T.sorted.markdup.recal.bam_NewCaptureRegions.bed

• Please ensure that your file is TAB delimited (e.g., cat -t FILE).
• Also ensure that your file has integer chromosome coordinates in the
  expected columns (e.g., cols 2 and 3 for BED).
  [mpileup] 1 samples in 1 input files
  ..If you have got an error at this step and a mini-pileup file is empty, check that you are using samtools v1.1 or later and provide a corresponding path in your config file
  [mpileup] 1 samples in 1 input files
  ..If you have got an error at this step and a mini-pileup file is empty, check that you are using samtools v1.1 or later and provide a corresponding path in your config file
  ... -> Done!

The ERROR indicated that "unable to open file or unable to determine types for file /home/ug0416/software/FREEC-11.6/data/output/SCA_082_T.sorted.markdup.recal.bam_NewCaptureRegions.bed"

The following is my config file:
###For more options see: http://boevalab.com/FREEC/tutorial.html#CONFIG ###

[general]
chrLenFile = /home/ug0416/software/FREEC-11.6/data/hg19.len
window = 0
ploidy = 2,3
outputDir = /home/ug0416/software/FREEC-11.6/data/output
bedtools = /pub/anaconda3/bin/bedtools
samtools = /home/ug0416/.conda/envs/sambamba/bin/samtools
#sex=XY
breakPointType=4
chrFiles = /home/ug0416/ref_hg19/ucsc_hg19_chromosome

maxThreads=6

breakPointThreshold=1.2
noisyData=TRUE
printNA=TRUE

readCountThreshold=60

[sample]

mateFile = /home/ug0416/mydata/05.gatk/a.BQSR/2nd_BQSR/SCA_082_T.sorted.markdup.recal.bam
inputFormat = BAM
mateOrientation = FR

[control]

mateFile = /home/ug0416/mydata/05.gatk/a.BQSR/2nd_BQSR/SCA_082_N.sorted.markdup.recal.bam
inputFormat = BAM
mateOrientation = FR

[BAF]

SNPfile = /home/ug0416/software/FREEC-11.6/data/hg19_snp142.SingleDiNucl.1based.txt
minimalCoveragePerPosition = 5
makePileup = /home/ug0416/software/FREEC-11.6/data/hg19_snp142.SingleDiNucl.1based.bed
fastaFile = /home/ug0416/ref_hg19/ucsc.hg19.fasta

[target]

captureRegions = /home/ug0416/software/FREEC-11.6/data/IDTV2.bed

I have no idea how to solve this issue. Hope your response! Appreciate!

[valeu]

Does your output directory have writing rights?
/home/ug0416/software/FREEC-11.6/data/output/

[dariober]

Maybe related: dariober/cnv_facets#45

Long story short: the input reads have been mistakenly aligned using the first-in-pair fastq file twice. This is going to cause all sorts of issues for any program.