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It asks for path to chromosome files, but I thought I provided those in the config file.
The output:
printing counts into /net/kodiak/volumes/delta/shared/prj/GELA20140221/cancer/runs/control-freec/GELS00000000006/20140319230000-reprocessed_config4/chr22/006T.chr22.pileup_sample.cpn
..Window size: 92758
..Will not consider chrY..
..Erased chrY from the list of chromosomes
..File /net/kodiak/volumes/river/shared/users/ltfang/link_to_reference/hg19.len was read
..Starting reading /net/kodiak/volumes/delta/shared/tmp/GELS0006/Reprocessed/006N.chr22.pileup
PROFILING [tid=140714407118624]: /net/kodiak/volumes/delta/shared/tmp/GELS0006/Reprocessed/006N.chr22.pileup read in 12 seconds [fillMyHash]
34369121 lines read..
14622030 reads used to compute copy number profile
printing counts into /net/kodiak/volumes/delta/shared/prj/GELA20140221/cancer/runs/control-freec/GELS00000000006/20140319230000-reprocessed_config4/chr22/006N.chr22.pileup_control.cpn
..Will not consider chrY..
..Erased chrY from the list of chromosomes
..using GC-content to normalize copy number profiles
Error: Uncorrect window size in the GC-content profile. FREEC will need to recalculate it. You must provide a path to chromosome files, option "chrFiles"
Any idea?
Code:
[general] #BedGraphOutput = TRUE #breakPointThreshold = 0.8 #breakPointType=2 chrLenFile = /net/kodiak/volumes/river/shared/users/ltfang/link_to_reference/hg19.len coefficientOfVariation = 0.05 contaminationAdjustment = TRUE GCcontentProfile = /net/kodiak/volumes/river/shared/users/ltfang/link_to_reference/GC_profile_50kb.cnp gemMappabilityFile = /net/kodiak/volumes/river/shared/users/ltfang/link_to_reference/out100m1_hg19.gem chrFiles = /net/kodiak/volumes/lake/shared/users/ltfang/chrFiles_hg19 minMappabilityPerWindow = 0.85 forceGCcontentNormalization = 2 ploidy = 2 intercept = 0 minCNAlength = 4 outputDir = /net/kodiak/volumes/delta/shared/prj/GELA20140221/cancer/runs/control-freec/GELS00000000006/20140319230000-reprocessed_config4/chr22 degree=3 maxThreads = 2 #readCountThreshold=10 samtools = /net/kodiak/volumes/lake/shared/opt/samtools/samtools sex = XX #telocentromeric=50000 uniqueMatch=TRUE [sample] mateFile = /net/kodiak/volumes/delta/shared/tmp/GELS0006/Reprocessed/006T.chr22.pileup inputFormat = pileup mateOrientation = FR [control] mateFile = /net/kodiak/volumes/delta/shared/tmp/GELS0006/Reprocessed/006N.chr22.pileup inputFormat = pileup mateOrientation = FR [BAF] SNPfile = /net/kodiak/volumes/river/shared/users/ltfang/link_to_reference/hg19_snp131.SingleDiNucl.1based.txt minimalCoveragePerPosition = 5
The output:
printing counts into /net/kodiak/volumes/delta/shared/prj/GELA20140221/cancer/runs/control-freec/GELS00000000006/20140319230000-reprocessed_config4/chr22/006T.chr22.pileup_sample.cpn
..Window size: 92758
..Will not consider chrY..
..Erased chrY from the list of chromosomes
..File /net/kodiak/volumes/river/shared/users/ltfang/link_to_reference/hg19.len was read
..Starting reading /net/kodiak/volumes/delta/shared/tmp/GELS0006/Reprocessed/006N.chr22.pileup
PROFILING [tid=140714407118624]: /net/kodiak/volumes/delta/shared/tmp/GELS0006/Reprocessed/006N.chr22.pileup read in 12 seconds [fillMyHash]
34369121 lines read..
14622030 reads used to compute copy number profile
printing counts into /net/kodiak/volumes/delta/shared/prj/GELA20140221/cancer/runs/control-freec/GELS00000000006/20140319230000-reprocessed_config4/chr22/006N.chr22.pileup_control.cpn
..Will not consider chrY..
..Erased chrY from the list of chromosomes
..using GC-content to normalize copy number profiles
Error: Uncorrect window size in the GC-content profile. FREEC will need to recalculate it. You must provide a path to chromosome files, option "chrFiles"
Any idea?
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