I didn't get any of these files: _CNV. , _BAF.txt, ratio.txt #160
Description
Hi, I am using FreeC v11.6b. with command line freec -conf /config_CNS-P0001.txt ,
I only get these files as output:
AN_control.cpn
PT_sample.cpn
GC_profile.50000bp.cnp
I didn't get any of these files: _CNV. , _BAF.txt, ratio.txt,......... although it is been around 48 hrs running on the HPC.
Would you help please?
The config file contains:
[general]
outputDir = /results/freec
BedGraphOutput = TRUE
chrLenFile = /selected_chr.fa.fai
ploidy = 2,3,4
coefficientOfVariation = 0.05
window = 50000
chrFiles = /chromosomes/final
sex=XX
[sample]
mateFile = /CNS-P0001_PT_sorted.bam
miniPileup = /CNS-P0001_PT.miniPileup
inputFormat = BAM
mateOrientation = FR
[control]
mateFile = /CNS-P0001_AN_sorted.bam
miniPileup =/CNS-P0001_AN.miniPileup
inputFormat = BAM
[BAF]
SNPfile = /CNS-P0001_AN.bed
The files used in the config txt as following:
chrLenFile
chr1 248956422 112 70 71
chr2 242193529 252513167 70 71
chr3 198295559 498166716 70 71
chr4 190214555 699295181 70 71
chr5 181538259 892227221 70 71
chr6 170805979 1076358996 70 71
chr7 159345973 1249605173 70 71
chr8 145138636 1411227630 70 71
chr9 138394717 1558439788 70 71
chr10 133797422 1698811686 70 71
chr11 135086622 1834520613 70 71
chr12 133275309 1971537157 70 71
chr13 114364328 2106716512 70 71
chr14 107043718 2222714743 70 71
chr15 101991189 2331287770 70 71
chr16 90338345 2434736088 70 71
chr17 83257441 2526365093 70 71
chr18 80373285 2610812039 70 71
chr19 58617616 2692333639 70 71
chr20 64444167 2751788762 70 71
chr21 46709983 2817153685 70 71
chr22 50818468 2864531079 70 71
chrX 156040895 2916075638 70 71
chrY 57227415 3074345836 70 71
chrFiles
chr10.fasta chr12.fasta chr14.fasta chr16.fasta chr18.fasta chr1.fasta chr21.fasta chr2.fasta chr4.fasta chr6.fasta chr8.fasta chrM.fasta chrY.fasta chr11.fasta chr13.fasta chr15.fasta chr17.fasta chr19.fasta chr20.fasta chr22.fasta chr3.fasta chr5.fasta chr7.fasta chr9.fasta chrX.fasta
mateFile = /CNS-P0001_PT_sorted.bam
samtools view /CNS-P0001_PT_sorted.bam | head
A01410:43:HWNCGDSX2:1:1161:19199:12915 113 chr1 9996 0 96S55M chr18 80263104 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCTACCCTTTTCAAGCAGCATACCGCTTACGATATCTCCATCTGTTACGGTATTTCTTACGTTTTCTCTTCCGATATCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA FFF,F::::,F,,,:,F,F:,,:::,::,,,,:,,F,:F,,,F:,,,:,F,:,:,,F,,,FF,:,,FF:,:F:FF,,,F,:F:,FFF:F,:,F,,F:,F,:F,FF,:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:1 MD:Z:7A47 AS:i:50 XS:i:47 SA:Z:chr2,32916441,+,121S30M,0,0; RG:Z:SPR-PCB-CNS-P0001_PT
A01410:43:HWNCGDSX2:1:1176:21124:35634 145 chr1 9996 14 108S43M = 180811 170774 CCCCCCCCCCCCCCCCCCCCCCCCTCTTAATGATACCCCCCCCTCCTATTACTACCCGTTTATTTTTAATATTACCATTAAACTCTCTCTTCCGATATACCTATCTCTTCCGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA F,FFFFFFF:F:FFFF:F:FFF:,,,,,F,,:F,,F,,:,,,,,,,,F:,,,:,,,F,,,,F,,F,,,,,,:,,FF,,,,,,,,::F:FFF,F:,F:,,:,F,,F,FF,,:,:F:,FFFFF,FFFFFF:FFFFFFFFFFFFFFFFFFFFFF NM:i:0 MD:Z:43 AS:i:43 XS:i:39 XA:Z:chr6,-147869,112S39M,0;chr15,+101981091,38M113S,0;chr7,-10002,113S38M,0;chr1,-180752,113S38M,0;chr7_KI270899v1_alt,-2,113S38M,0; RG:Z:CNS-P0001_PT
miniPileup = /CNS-P0001_PT.miniPileup
this minipile up generated from sambamba_v0.5.9 mpileup -t 16 -o normal.miniPileup normal.bam
--samtools -f /gpfs/data_jrnas1/ref_data/Hsapiens/hg38/seq_bwa/hg38.fa -d 8000 -Q 0 -q 1 -l snps.bed
head /CNS-P0001_PT.miniPileup
chr1 54844 G 101 ,.,.,,,..aAAAAAAaaaaa,,,,AA,a.AAa,AAA,AAA,a..,,AA,AA,.aA.,..,.AA,A.,.aa.a..AA,,.,,a,aa,.,,,,,aaa,,,,, FFF:FFFF,F8FFFFFFF9FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFkFFFFF:FF:FF:FF:FFFFFFFFF!FF:FFFFFFFFFFFFFFFF
chr1 55299 C 66 TTTTTTTtTttttTtttTtTtTtTTTTtttttttTTtttTTTtttTtTtttttTtttTtttTTTtt (FFFFFFF,FFFFFFFFkFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF!FFF))
SNPfile = /CNS-P0001_AN.bed
this snp file generated by GATK from the normal sample
head /CNS-P0001_AN.bed
chr1 15819 15820 G T
chr1 16287 16288 C G
chr1 16297 16298 C T
chr1 54365 54366 A G
chr1 54379 54380 T C
chr1 54585 54586 T C
chr1 54675 54676 C T
chr1 54707 54708 G C
chr1 54843 54844 G A
chr1 55298 55299 C T