Control-FREEC question

[lethalfang]

It asks for path to chromosome files, but I thought I provided those in the config file.

[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?

[TiborNagy]

What kind of files can be found on /net/kodiak/volumes/lake/shared/users/ltfang/chrFiles_hg19?

[lethalfang]

What kind of files can be found on /net/kodiak/volumes/lake/shared/users/ltfang/chrFiles_hg19?

They are symbolic links to chr1.fa, chr1.fa.fai, chr2.fa, chr2.fa.fai, ...., chrY.fa, chrY.fa.fai.