Hi,
I am using control-FREEC to analyze a few mouse WES samples to get the CNVs.
I went through the manual and created config_ctrl file as suggested in the manual and the previous posts here, but I still encounter one error message and I couldn't figure out why.
Greatly appreciate if anyone can help me with it. Thanks a lot in advance!
Thanks a lot!!!
Yihua
I am using control-FREEC to analyze a few mouse WES samples to get the CNVs.
I went through the manual and created config_ctrl file as suggested in the manual and the previous posts here, but I still encounter one error message and I couldn't figure out why.
Greatly appreciate if anyone can help me with it. Thanks a lot in advance!
Code:
Control-FREEC v7.2 : calling copy number alterations and LOH regions using deep-sequencing data MT-mode using 6 threads ..Minimal CNA length (in windows) is 4 ..Breakpoint threshold for segmentation of copy number profiles is 0.8 ..Polynomial degree for "ReadCount ~ GC-content" or "Sample ReadCount ~ Control ReadCount" is 3 ..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 going to adjust profiles for a possible contamination by normal cells ..set contaminationAdjustment=FALSE if you don't want to use this option because you think that there is no contamiantion of your tumor sample by normal cells (e.g., it is a cell line, or it non-cancer DNA used without a control sample) ..FREEC is going to evaluate contamination by normal cells ..Note, the Coefficient Of Variation won't be used since "window" = 8000 was set ..Step: 2500 ..Output directory: /rsrch1/epi/scheet/PROJECTS/Kadara_Mouse/working/FreeC/pilot/working/results/ ..Sample file: /rsrch1/epi/scheet/PROJECTS/Kadara_Mouse/working/sequenza/pilot/0001-samtools-prep/output/S08.pileup.gz ..Sample input format: pileup ..Control file: /rsrch1/epi/scheet/PROJECTS/Kadara_Mouse/working/sequenza/pilot/0001-samtools-prep/output/S01.pileup.gz ..Input format for the control file: pileup ..File with chromosome lengths: /rsrch1/epi/scheet/PROJECTS/Kadara_Mouse/working/FreeC/pilot/control/mouse_chr_y.len ..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 ..File /rsrch1/epi/scheet/PROJECTS/Kadara_Mouse/working/FreeC/pilot/control/mouse_chr_y.len was read ..Starting reading /rsrch1/epi/scheet/PROJECTS/Kadara_Mouse/working/sequenza/pilot/0001-samtools-prep/output/S08.pileup.gz PROFILING [tid=140174374557472]: /rsrch1/epi/scheet/PROJECTS/Kadara_Mouse/working/sequenza/pilot/0001-samtools-prep/output/S08.pileup.gz read in 155 seconds [fillMyHash] 260591386 lines read.. 47399307 reads used to compute copy number profile printing counts into /rsrch1/epi/scheet/PROJECTS/Kadara_Mouse/working/FreeC/pilot/working/results/S08.pileup.gz_sample.cpn ..Window size: 8000 ..File /rsrch1/epi/scheet/PROJECTS/Kadara_Mouse/working/FreeC/pilot/control/mouse_chr_y.len was read ..Starting reading /rsrch1/epi/scheet/PROJECTS/Kadara_Mouse/working/sequenza/pilot/0001-samtools-prep/output/S01.pileup.gz PROFILING [tid=140174374557472]: /rsrch1/epi/scheet/PROJECTS/Kadara_Mouse/working/sequenza/pilot/0001-samtools-prep/output/S01.pileup.gz read in 202 seconds [fillMyHash] 278748064 lines read.. 68986773 reads used to compute copy number profile printing counts into /rsrch1/epi/scheet/PROJECTS/Kadara_Mouse/working/FreeC/pilot/working/results/S01.pileup.gz_control.cpn ..will remove all windows with read count in the control less than 50 Initial guess for polynomial: Error: variation in read count per window is too small. Unable to proceed..
Yihua
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