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No figures created, no CNV's called. #7

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pineapple216 opened this issue Jul 27, 2015 · 3 comments
Open

No figures created, no CNV's called. #7

pineapple216 opened this issue Jul 27, 2015 · 3 comments

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@pineapple216
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Hi Shilin,

I've managed to run ExonDel without errors.
It finishes without giving any errors.

The console output can be seen hereunder:

[Mon Jul 27 10:55:47 2015] All genes will be used
[Mon Jul 27 10:55:47 2015] Loading BED file
[Mon Jul 27 10:55:47 2015] Finish BED file (cover 21634 base pairs)
[Mon Jul 27 10:55:47 2015] Loading RefSeq file
[Mon Jul 27 10:55:51 2015] Finish RefSeq file
[Mon Jul 27 10:55:51 2015] Loading fasta file and caculating GC content
[Mon Jul 27 10:56:10 2015] Caculating GC content in 13: 27 exons
[Mon Jul 27 10:56:13 2015] Caculating GC content in 17: 136 exons
[Mon Jul 27 10:56:18 2015] Finish fasta file
[Mon Jul 27 10:56:18 2015] Loading genesPassQCwithGC.bed
[Mon Jul 27 10:56:18 2015] Processing bam files
[Mon Jul 27 10:56:18 2015] Thread 1 stared
[Mon Jul 27 10:56:18 2015] Thread 1 processing /home/koen/new_BRCA_runs/150710_NS500265_0100_AH3LL2AFXX/DNA04-04209_BRCA1_R15-12598_B8_17151464.bam DNA04-04209_BRCA1_R15-12598_B8_171514
64
[Mon Jul 27 10:56:18 2015] Thread 2 stared
[Mon Jul 27 10:56:18 2015] Thread 2 processing /home/koen/new_BRCA_runs/150710_NS500265_0100_AH3LL2AFXX/DNA04-04209_BRCA1_R15-12598_E7_17151463.bam DNA04-04209_BRCA1_R15-12598_E7_171514
63

etc. etc.

It then finishes with:

[Mon Jul 27 10:57:54 2015] Thread 1 finished
[Mon Jul 27 10:58:04 2015] Thread 2 finished
[Mon Jul 27 10:58:04 2015] Thread 3 finished
[Mon Jul 27 10:58:04 2015] Thread 4 finished
[Mon Jul 27 10:58:04 2015] Thread 5 finished
[Mon Jul 27 10:58:04 2015] Thread 6 finished
[Mon Jul 27 10:58:15 2015] Thread 7 finished
[Mon Jul 27 10:58:15 2015] Thread 8 finished
[Mon Jul 27 10:58:15 2015] Thread 9 finished
[Mon Jul 27 10:58:15 2015] Thread 10 finished
[Mon Jul 27 10:58:15 2015] Thread 11 finished
[Mon Jul 27 10:58:15 2015] Thread 12 finished
[Mon Jul 27 10:58:15 2015] Thread 13 finished
[Mon Jul 27 10:58:15 2015] Thread 14 finished
[Mon Jul 27 10:58:15 2015] Thread 15 finished
[Mon Jul 27 10:58:15 2015] Finish bam file
[Mon Jul 27 10:58:15 2015] Analyzing Exon Deletion
[Mon Jul 27 10:58:17 2015] Success!

My config file contains;

config file for ExonDel software

[perl]

reference .bed file

bedfile=/home/koen/cnv_tool_comparison/reference_files/BRCA_1_2_new_mip_panel_sorted_merged_only_normal_mips.bed

reference .gtf file

refseq=/home/koen/cnv_tool_comparison/reference_files/refGene.hg19.24feb2015ucsc.gtf

reference .fa file

reffa=/data/references/hg19/ref_hg19.fasta

Minimal percent of covered base pairs for each exon

exon_bp_cover_threshold=0.1

Minimal percent of covered exons for each gene. 1 means 100%

overall_exon_count_threshold=0.001

Minimum mapping quality for an alignment to be used

mapQ=20

Minimum base quality for a base to be considered

baseQ=20

where the R bin file is

RBin=R

where the SAMtools bin file is

samtoolsBin=samtools

name of the log file

logFileName=ExonDel.log
[R]

Maximal number of exons for the moving-window in exon deletion detection

maxWinLength=23

Minimum number of exons for the moving-window in exon deletion detection

minWinLength=1

Minimum number of exons for a gene to be considered in exon deletion detection

minExonNum=1

T means True and F means False. If only some genes were used (use -g option), GC adjustment will not be performed no matter what adjustGC below was set (As GC adjustment is based on all ge

nes).
adjustGC=T

If all genes were used (didn't use -g option), cutoff 1,2 will be determined by cutoffQuantile 1,2 in all genes

cutoffQuantile1=0.01
cutoffQuantile2=0.1

If only some genes were used (use -g option), cutoff 1,2 will be determined by constant cutoff 1,2 below

cutoff1=2
cutoff2=20

All files, covered_percentage, genespassqc.bed(.bed.depth.all, .bed.depth.all.adjustGC), they're all there.

The only thing is that ExonDel doesn't call any CNV's, i.e. there are no figures being created and the results in the html report are empty.Some of my samples do have a CNV, so they should be called.

I hope to hear from you soon!

Best,

Koen
@slzhao
Copy link
Owner

slzhao commented Jul 27, 2015

Hello Koen,

Is there any exonDelsBy1.csv or exonDelsCutoffs.csv file?
You mentioned some of the samples have CNV, what is the content for the CNV
regions in your ".bed.depth.all", ".bed.depth.all.adjustGC" files?

Best,
Shilin

2015-07-27 7:05 GMT-05:00 Koen Hendriks notifications@github.com:

Hi Shilin,

I've managed to run ExonDel without errors.
It finishes without giving any errors.

The console output can be seen hereunder:

[Mon Jul 27 10:55:47 2015] All genes will be used
[Mon Jul 27 10:55:47 2015] Loading BED file
[Mon Jul 27 10:55:47 2015] Finish BED file (cover 21634 base pairs)
[Mon Jul 27 10:55:47 2015] Loading RefSeq file
[Mon Jul 27 10:55:51 2015] Finish RefSeq file
[Mon Jul 27 10:55:51 2015] Loading fasta file and caculating GC content
[Mon Jul 27 10:56:10 2015] Caculating GC content in 13: 27 exons
[Mon Jul 27 10:56:13 2015] Caculating GC content in 17: 136 exons
[Mon Jul 27 10:56:18 2015] Finish fasta file
[Mon Jul 27 10:56:18 2015] Loading genesPassQCwithGC.bed
[Mon Jul 27 10:56:18 2015] Processing bam files
[Mon Jul 27 10:56:18 2015] Thread 1 stared
[Mon Jul 27 10:56:18 2015] Thread 1 processing
/home/koen/new_BRCA_runs/150710_NS500265_0100_AH3LL2AFXX/DNA04-04209_BRCA1_R15-12598_B8_17151464.bam
DNA04-04209_BRCA1_R15-12598_B8_171514
64
[Mon Jul 27 10:56:18 2015] Thread 2 stared
[Mon Jul 27 10:56:18 2015] Thread 2 processing
/home/koen/new_BRCA_runs/150710_NS500265_0100_AH3LL2AFXX/DNA04-04209_BRCA1_R15-12598_E7_17151463.bam
DNA04-04209_BRCA1_R15-12598_E7_171514
63

etc. etc.

It then finishes with:

[Mon Jul 27 10:57:54 2015] Thread 1 finished
[Mon Jul 27 10:58:04 2015] Thread 2 finished
[Mon Jul 27 10:58:04 2015] Thread 3 finished
[Mon Jul 27 10:58:04 2015] Thread 4 finished
[Mon Jul 27 10:58:04 2015] Thread 5 finished
[Mon Jul 27 10:58:04 2015] Thread 6 finished
[Mon Jul 27 10:58:15 2015] Thread 7 finished
[Mon Jul 27 10:58:15 2015] Thread 8 finished
[Mon Jul 27 10:58:15 2015] Thread 9 finished
[Mon Jul 27 10:58:15 2015] Thread 10 finished
[Mon Jul 27 10:58:15 2015] Thread 11 finished
[Mon Jul 27 10:58:15 2015] Thread 12 finished
[Mon Jul 27 10:58:15 2015] Thread 13 finished
[Mon Jul 27 10:58:15 2015] Thread 14 finished
[Mon Jul 27 10:58:15 2015] Thread 15 finished
[Mon Jul 27 10:58:15 2015] Finish bam file
[Mon Jul 27 10:58:15 2015] Analyzing Exon Deletion
[Mon Jul 27 10:58:17 2015] Success!

My config file contains;

#config file for ExonDel software
[perl]
#reference .bed file

bedfile=/home/koen/cnv_tool_comparison/reference_files/BRCA_1_2_new_mip_panel_sorted_merged_only_normal_mips.bed
#reference .gtf file

refseq=/home/koen/cnv_tool_comparison/reference_files/refGene.hg19.24feb2015ucsc.gtf
#reference .fa file
reffa=/data/references/hg19/ref_hg19.fasta
#Minimal percent of covered base pairs for each exon
exon_bp_cover_threshold=0.1
#Minimal percent of covered exons for each gene. 1 means 100%
overall_exon_count_threshold=0.001
#Minimum mapping quality for an alignment to be used
mapQ=20
#Minimum base quality for a base to be considered
baseQ=20
#where the R bin file is
RBin=R
#where the SAMtools bin file is
samtoolsBin=samtools
#name of the log file
logFileName=ExonDel.log
[R]
#Maximal number of exons for the moving-window in exon deletion detection
maxWinLength=23
#Minimum number of exons for the moving-window in exon deletion detection
minWinLength=1
#Minimum number of exons for a gene to be considered in exon deletion
detection
minExonNum=1
#T means True and F means False. If only some genes were used (use -g
option), GC adjustment will not be performed no matter what adjustGC below
was set (As GC adjustment is based on all ge
nes).
adjustGC=T
#If all genes were used (didn't use -g option), cutoff 1,2 will be
determined by cutoffQuantile 1,2 in all genes
cutoffQuantile1=0.01
cutoffQuantile2=0.1
#If only some genes were used (use -g option), cutoff 1,2 will be
determined by constant cutoff 1,2 below
cutoff1=2
cutoff2=20

All files, covered_percentage, genespassqc.bed(.bed.depth.all,
.bed.depth.all.adjustGC), they're all there.

The only thing is that ExonDel doesn't call any CNV's, i.e. there are no
figures being created and the results in the html report are empty.Some of
my samples do have a CNV, so they should be called.

I hope to hear from you soon!

Best,

Koen

—
Reply to this email directly or view it on GitHub
#7.

@pineapple216
Copy link
Author

Hi Shilin,

exonDelsBy1.csv is not present.
exonDelsCutoffs.csv is and contains:

"cutoff","DNA04-04209_BRCA1_R15-12598_B8_17151464","DNA04-04209_BRCA1_R15-12598_E7_17151463","DNA13-03669_p-BRC_R15-12944_F2_17180520", etc. etc. my samples names

"cutoff1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0"
,"0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0"
"cutoff2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0"
,"0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0"

the latter metioned files (.bed.depth.all, .bed.depth.all.adjustGC) contain this for my region of interest

17 41242960 41243049 BRCA1 NR_027676 0.49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41243451 41246877 BRCA1 NR_027676 0.39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41247862 41247939 BRCA1 NR_027676 0.42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41249260 41249306 BRCA1 NR_027676 0.37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41251791 41251894 BRCA1 NR_027676 0.46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41256138 41256278 BRCA1 NR_027676 0.37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41256884 41256973 BRCA1 NR_027676 0.39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41258494 41258550 BRCA1 NR_027676 0.43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41267742 41267796 BRCA1 NR_027676 0.44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41276033 41276132 BRCA1 NR_027676 0.36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41277198 41277340 BRCA1 NR_027676 0.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41196311 41197819 BRCA1 NM_007300 0.44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

So it seems there's nothing being called.

If you need more information, please contact me!

Best,

Koen

@slzhao
Copy link
Owner

slzhao commented Aug 6, 2015

Hi Koen,

The ExonDel software is designed to find the exon deletions in genes, not
for CNV. So we require that there should be some reads for that gene to be
considered in exon deletion detection detection. That's why BRCA1 in your
result is not reported in the result.

Best,
Shilin

2015-07-28 1:43 GMT-05:00 Koen Hendriks notifications@github.com:

Hi Shilin,

exonDelsBy1.csv is not present.
exonDelsCutoffs.csv is and contains:

"cutoff","DNA04-04209_BRCA1_R15-12598_B8_17151464","DNA04-04209_BRCA1_R15-12598_E7_17151463","DNA13-03669_p-BRC_R15-12944_F2_17180520",
etc. etc. my samples names

"cutoff1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0"
,"0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0"

"cutoff2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0"
,"0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0"

the latter metioned files (.bed.depth.all, .bed.depth.all.adjustGC)
contain this for my region of interest

17 41242960 41243049 BRCA1 NR_027676 0.49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41243451 41246877 BRCA1 NR_027676 0.39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41247862 41247939 BRCA1 NR_027676 0.42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41249260 41249306 BRCA1 NR_027676 0.37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41251791 41251894 BRCA1 NR_027676 0.46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41256138 41256278 BRCA1 NR_027676 0.37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41256884 41256973 BRCA1 NR_027676 0.39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41258494 41258550 BRCA1 NR_027676 0.43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41267742 41267796 BRCA1 NR_027676 0.44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41276033 41276132 BRCA1 NR_027676 0.36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41277198 41277340 BRCA1 NR_027676 0.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0
17 41196311 41197819 BRCA1 NM_007300 0.44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

So it seems there's nothing being called.

If you need more information, please contact me!

Best,

Koen

—
Reply to this email directly or view it on GitHub
#7 (comment).

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@slzhao @pineapple216