rahmanteam / decon

Dr. Anna Fowler is the lead developer of DECoN and is continuing to support the software

decon's Issues

plan to make a conda version of decon?

Dear professor,
do you plan to make a conda version of decon, thanks a lot

ERROR IN CNV

Problem installing DECoN on ubuntu Failed to install VGAM (0.9-8)

Hi

I have downloaded the zip file from this location, and extracted it.

Then, in the folder I executed

sudo ./setup.sh

and this is the log that is generated.

* installing *source* package ‘packrat’ ...
** package ‘packrat’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (packrat)
Installing BiocGenerics (0.12.1) ... OK (built source)
Installing DBI (0.3.1) ... OK (built source)
Installing R.methodsS3 (1.7.0) ... OK (built source)
Installing R6 (2.0.1) ... OK (built source)
Installing RColorBrewer (1.1-2) ... OK (built source)
Installing RJSONIO (1.3-0) ... OK (built source)
Installing Rcpp (0.11.6) ... OK (built source)
Installing VGAM (0.9-8) ... Error in installPkg(pkgRecord, project, availablePkgs, repos, lib, cache) : 
  Failed to install VGAM (0.9-8): sources missing at /home/bioinfo/RahmanTeam-DECoN-8d740c5/Linux/packrat/src/VGAM/VGAM_0.9-8.tar.gz
Calls: <Anonymous> -> restoreImpl -> playActions -> installPkg
In addition: Warning message:
In packrat::restore() :
  The most recent snapshot was generated using R version 3.1.2
Execution halted

My R sessionInfo

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

locale:
 [1] LC_CTYPE=en_IN       LC_NUMERIC=C         LC_TIME=en_IN       
 [4] LC_COLLATE=en_IN     LC_MONETARY=en_IN    LC_MESSAGES=en_IN   
 [7] LC_PAPER=en_IN       LC_NAME=C            LC_ADDRESS=C        
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C 

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

loaded via a namespace (and not attached):
[1] tools_3.2.3

ERROR when running decon

Hi! I am trying to run decon but I get an error during the makeCNVcalls.R:

There were 50 or more warnings (use warnings() to see the first 50)
Error in Summary.factor(378L, na.rm = FALSE) :
‘min’ not meaningful for factors
Calls: unlist -> lapply -> FUN -> Summary.factor
Execution halted

Any ideas?

Error in makeCNVcalls

I can't seem to get the makeCNVcalls script to run properly. I changed the header names of the ExomeCount objects to reflect the update of the ExomeDepth package. However, I still seem to get the following error log.

Loading require```
d package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following objects are masked from ‘package:methods’:

    getClasses, getMethods

The following objects are masked from ‘package:base’:

    attach, detach, gc, load, save

R.utils v2.9.0 successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

    timestamp

The following objects are masked from ‘package:base’:

    cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
    warnings

[1] "BEGIN makeCNVCalls.R"
[1] "Processing sample: TN18-105679.recalreads.reheader 1/45"
Optimization of the choice of aggregate reference set, this process can take some time
Number of selected bins: 7021
Now fitting the beta-binomial model on a data frame with 8311 rows : this step can take a few minutes.
Now computing the likelihood for the different copy number states
Error in CallCNVs(x = all.exons, transition.probability = trans_prob,  : 
  Chromosome, start and end vector must have the same lengths.
Calls: CallCNVs -> CallCNVs
In addition: There were 22 warnings (use warnings() to see them)
Execution halted

Any help or fixes would be greatly appreciated.

Error RangedData objects are deprecated

Hi,
My R version is 3.6 and bioconductor is the latest version, I run into this error:

command:
Rscript --default-packages=methods,datasets,utils,grDevices,graphics,stats ReadInBams.R --bams bam --bed step1.bed.txt --fasta hg19.fa --out results

error:
[1] "BEGIN ReadInBams.R"
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
Registered S3 method overwritten by 'R.oo':
method from
throw.default R.methodsS3
R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following objects are masked from ‘package:methods’:

getClasses, getMethods

The following objects are masked from ‘package:base’:

attach, detach, gc, load, save

R.utils v2.9.0 successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

timestamp

The following objects are masked from ‘package:base’:

cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
warnings

[1] "bam"
Error: RangedData objects are deprecated and the rownames setter for
RangedData objects is now defunct. Please migrate your code to use
GRanges or GRangesList objects instead. See IMPORTANT NOTE in
?RangedData
In addition: Warning messages:
1: RangedData objects are deprecated. Please migrate your code to use
GRanges or GRangesList objects instead. See IMPORTANT NOTE in
?RangedData
2: RangedData objects are deprecated. Please migrate your code to use
GRanges or GRangesList objects instead. See IMPORTANT NOTE in
?RangedData
3: RangedData objects are deprecated. Please migrate your code to use
GRanges or GRangesList objects instead. See IMPORTANT NOTE in
?RangedData
4: RangedData objects are deprecated. Please migrate your code to use
GRanges or GRangesList objects instead. See IMPORTANT NOTE in
?RangedData
5: RangedData objects are deprecated. Please migrate your code to use
GRanges or GRangesList objects instead. See IMPORTANT NOTE in
?RangedData
6: RangedData objects are deprecated. Please migrate your code to use
GRanges or GRangesList objects instead. See IMPORTANT NOTE in
?RangedData
Execution halted

Thanks in advance!

DECoN installation error

"Failed to retrieve ExomeDepth package"

Please suggest how to resolve this issue and setup DECoN successfully.

makeCNV calls error in naming gene

Dear developers, we are using Decon to analyse our sample enriched with illumina trusight cancer panel.
We created a bed with a limited number of genes and we correctly created the corresponding custom file (cancer_panel_for_Decon_sorted.txt) . But we encountered an error when a cnv is present in BRCA1 gene, it is always associated to RAD51C gene but the coordinates in the txt files are correct and are the ones of BRCA2 (pdf file and CNVCalls_all.txt).
I tried launching Decon with only BRCA gene and the cnv is correctly associated and also considering only RAD51C the cnv is not detected.
Is there an explanation for this behaviour? I attached also a screenshot of some warning that the script raise.

Thanks a lot for the help

18-2920_S20_RGSorted_RAD51C.pdf
CNVCalls_all.txt
cancer_panel_for_Decon_sorted.txt

Error in makeCNVcall.R

Hello, I'm trying to run DECoN on Fedora, I followed the procedure in the manual and created the R image to load as input in the command in object, I just launched the command below:
/R-3.4.2/bin/Rscript makeCNVcalls.R --transProb 0.01 --Rdata test.out.RData --plot All --custom FALSE --plotFolder out_F

after computing all the CNV calls it gives me this error:

There were 13 warnings (use warnings() to see them)
Error in cnv.calls_ids[i, ]$start.p:cnv.calls_ids[i, ]$end.p :
result would be too long a vector
Inoltre: Warning messages:
1: In min(overlap) : no non-missing arguments to min; returning Inf
2: In max(overlap) : no non-missing arguments to max; returning -Inf
3: In min(overlap) : no non-missing arguments to min; returning Inf
4: In max(overlap) : no non-missing arguments to max; returning -Inf
5: In min(overlap) : no non-missing arguments to min; returning Inf
6: In max(overlap) : no non-missing arguments to max; returning -Inf
execution interrupted

What could be causing the error?

Thank you

CNV offsets by one in makeCNVcalls.

After having used the v1 for a long time, I coud not retrieve the CNVs after installing DECoN v2.

I first corrected the script IdentifyFailures.R as mention in the issue #40.
but in the next script makeCNVcalls.R there is actually the same issue.
Ligne 69:
colnames(ExomeCount)[1:length(sample.names)+4]=sample.names
it should be
colnames(ExomeCount)[1:length(sample.names)+5]=sample.names

Otherwise all the samples / CNV are offsets.

It would be great to fix both of these issues in the git.

ERROR when running makeCNVcalls.R

--Hello,

execution halted with:

[1] "BEGIN makeCNVCalls.R"
[1] "Processing sample: SRR098401 1/2"
Optimization of the choice of aggregate reference set, this process can take some time
Number of selected bins: 10000
Error in data.frame(ref.samples = dimnames(reference.counts)[[2]], correlations = my.correlations, :
arguments imply differing number of rows: 0, 1
Calls: select.reference.set -> data.frame
Execution halted

what's wrong ?

Congratulations!

A big update to the new verison!
I have been working on installing this tool these days, even via docker...But failed. When I reload the github page this morning, here comes the v2 verison... What a wonderful world...

Thank you.^_^.
xiucz

Working out which samples had strong correlation

Hello,

Is there a way to work out which samples were used as part of the reference set for making a CNV call? The only information easily accessible is the number used in "comp" column. I am using Rstudio and when it opens up CNVcalls*.Rdata it has difficulty in parsing it in a sensible format.

Any advise or commands to use, to extract the individual detail would be helpful. Thanks in advance.

Sanjeev

Using DECoN with two samples

I would like to test the makeCNVcalls script. According to the manual for ExomeDepth it is recommended to have 5 - 10 samples. I am wondering if it is possible to use DECoN if I have only two samples (matched sample and control).

Thanks!

error when running ReadInBams.R

my command is as follows:

export PATH='/home/wubin/01.Program/02.software/R-3.1.2/bin':$PATH

export R_LIBS_USER='/mnt/lustre/user/wubin/01.Program/Scripts/02.software/DECoN/Linux/packrat/lib/x86_64-unknown-linux-gnu/3.1.2'
export R_LIBS_USER=$R_LIBS_USER:'/mnt/lustre/user/wubin/01.Program/Scripts/02.software/DECoN/Linux/packrat/lib-ext'
export R_LIBS_USER=$R_LIBS_USER:'/home/wubin/01.Program/02.software/R-3.1.2/library'
#cd /mnt/lustre/user/wubin/01.Program/Scripts/02.software/DECoN/Linux
Rscript /mnt/lustre/user/wubin/01.Program/Scripts/02.software/DECoN/Linux/ReadInBams.R --bams /home/wubin/05.tests/DECoN/bams/bamList.txt --bed /mnt/lustre/user/wubin/01.Program/Scripts/01.script/GeneLab/Config/bed/BGI171.CNV_Analysis.bed --fasta /mnt/lustre/user/wubin/01.Program/Scripts/02.software/GATK/fasta_index/hg19.fa --out /home/wubin/05.tests/DECoN/bams/test_result/DECoNtest

and the error is:

Initializing packrat project in directory:

• "/home/wubin/05.tests/DECoN"
  Error in if (result$source == "unknown" && fallback.ok) { :
  missing value where TRUE/FALSE needed
  Calls: ... getPackageRecords -> getPackageRecordsExternalSource -> lapply -> FUN
  In addition: There were 50 or more warnings (use warnings() to see the first 50)
  Execution halted
  ===============================================================

I don't know what the real problem is

Error when running makeCNVcalls.R

I ran command "Rscript --default-packages=methods,datasets,utils,grDevices,graphics,stats makeCNVcalls.R --Rdata /mac/decov.results.RData --transProb 0.01 --custom TRUE --out /mac/result.call.cnv --plot All --plotFolder /mac/DECoNPlots --exons /mac/H27_exon_coverage_v1.0.1_20210317_sorted_edit_decov.bed" and got the following issue.
It seems from the R package "ExomeDepth"

makeCNVcalls.R Error in cnv.calls_ids[i, ]$start.p:cnv.calls_ids[i, ]$end.p :

I have 185 female and 214 male WES samples, I successfully run female samples and no errors, but when I run 214 male samples in the makeCNVcalls.R step, Error shows :
ERROR Error in cnv.calls_ids[i, ]$start.p:cnv.calls_ids[i, ]$end.p :

command:
$Rscript makeCNVcalls.R --Rdata male.RData --custom FALSE --out male_DECoNCalls --plot None --plotFolder DECoNPlots

end of the log file:
[1] "Processing sample: PxxxF.rmdup 214/214"
Optimization of the choice of aggregate reference set, this process can take some time
Number of selected bins: 10000
Now fitting the beta-binomial model on a data frame with 243190 rows : this step can take a few minutes.
Now computing the likelihood for the different copy number states
Correlation between reference and tests count is 0.99024
To get meaningful result, this correlation should really be above 0.97. If this is not the case, consider the output of ExomeDepth as less reliable (i.e. most likely a high false positive rate)
Number of calls for chromosome 1 : 64
Number of calls for chromosome 2 : 39
Number of calls for chromosome 3 : 12
Number of calls for chromosome 4 : 26
Number of calls for chromosome 5 : 27
Number of calls for chromosome 6 : 26
Number of calls for chromosome 7 : 56
Number of calls for chromosome 8 : 23
Number of calls for chromosome 9 : 25
Number of calls for chromosome 10 : 29
Number of calls for chromosome 11 : 17
Number of calls for chromosome 12 : 28
Number of calls for chromosome 13 : 2
Number of calls for chromosome 14 : 20
Number of calls for chromosome 15 : 48
Number of calls for chromosome 16 : 44
Number of calls for chromosome 17 : 23
Number of calls for chromosome 18 : 10
Number of calls for chromosome 19 : 54
Number of calls for chromosome 20 : 5
Number of calls for chromosome 21 : 8
Number of calls for chromosome 22 : 27
Number of calls for chromosome X : 23
Number of calls for chromosome Y : 3
There were 50 or more warnings (use warnings() to see the first 50)
Error in cnv.calls_ids[i, ]$start.p:cnv.calls_ids[i, ]$end.p :
答案矢量会太长
此外: There were 50 or more warnings (use warnings() to see the first 50)
停止执行

I don't know why, Please help me to figure out. thanks a lot!

Problem while running Rscript makeCNVcalls.R

Dear All,

I have successfully installed Decon in my PC and encountering below mentioned error while executing Rscript makeCNVcalls.R command:

• The library is already synchronized with the lockfile.
  Loading required package: R.oo
  Loading required package: R.methodsS3
  R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following object is masked from ‘package:R.methodsS3’:

throw

The following objects are masked from ‘package:methods’:

getClasses, getMethods

The following objects are masked from ‘package:base’:

attach, detach, load, save

R.utils v2.11.0 (2021-09-26 08:30:02 UTC) successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

timestamp

The following objects are masked from ‘package:base’:

cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
warnings

[1] "BEGIN makeCNVCalls.R"
Error in getopt_options(object, args) :
Error in getopt(spec = spec, opt = args) : long flag "Rdata" is invalid
Calls: parse_args -> parse_options -> getopt_options
Execution halted

Any solution for this problem?

Your help would be highly appreciated.

Thank you
Bala

Error in ReadInBams (GenomicRanges::seqnames(target))

Hello:

I am running DECoN in Windows, but we are having a lot of errors in the execution of ReadInBams.bat. This is the error:
"Error in GenomicRanges::seqnames(target) : error in evaluating the argument 'x' in selecting a method for function 'seqnames': Error: object target not found"

Our inputs are the BAM files, the .bed file (without the "chr" prefix, due to previous errors we eliminated the prefix) and the reference fasta file in .fa format. We cannot find a solution for this, so if anybody had this error or knows how to solve it, we would very much appreciate it.

Error in running IdentifyFailures

In IdentifyFailures.R，Somtimes have error "Error in `[.default`(exons$Custom.Exon, a) : invalid subscript type 'list'  "

I fount the reason: "a" is a list, exons$Custom[a] can not return values from a list.
Can you fix it ?

151 Brca<-which(colSums(brca)!=0)
152
153 a<-apply(brca[,Brca,drop=F],2,which)
154
155 Clinical_Numbering=rep("NA",length(Exon))
156
157 Clinical_Numbering[paste(Exon)%in%row.names(failed.calls[Brca,])] = exons$Custom[a]

Installing DECoN on win10

Hi all,
I was successful with installing and running DECoN on Linux, however, now I am trying to install it on Windows 10 and cannot do it.
I did following:

1. I installed R-3.2 and added it to the system path variable
2. I installed Rtools32 and added it to the system path variable
3. I run DECoN setup.bat script (DECoN-v1.0.2) as admin and obtained following message

Checking your default version of R
R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
default
Running setup scripts...
unable to open output file
Press any key to continue . . .

Do someone have an experience with this?

makeCNVcalls.R failed

failed again with:

[1] "BEGIN makeCNVCalls.R"
[1] "Processing sample: SRR6823378_recalibrated 1/5"
Optimization of the choice of aggregate reference set, this process can take some time
Number of selected bins: 10000
Now fitting the beta-binomial model on a data frame with 206472 rows : this step can take a few minutes.
Now computing the likelihood for the different copy number states
Error in CallCNVs(x = all.exons, transition.probability = trans_prob, :
Chromosome, start and end vector must have the same lengths.
Calls: CallCNVs -> CallCNVs
In addition: Warning messages:
1: In aod::betabin(data = data.for.fit, formula = as.formula(formula), :
The data set contains at least one line with weight = 0.

2: In aod::betabin(data = data.for.fit, formula = as.formula(formula), :
The data set contains at least one line with weight = 0.

3: In aod::betabin(data = data.for.fit, formula = as.formula(formula), :
The data set contains at least one line with weight = 0.

Execution halted

Failed installation

Hello,

I am trying to install DECoN on my Mac (macOS Catalina 10.15.2). I already have gcc (installed with homebrew) and gfortran seems to be included in the gcc installation. I then try to run the setup.sh, and lots of connection errors start to appear:
_* installing source package ‘packrat’ ...
** package ‘packrat’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

• DONE (packrat)
  Warning: unable to access index for repository http://bioconductor.org/packages/3.0/bioc/bin/macosx/el-capitan/contrib/3.5:
  no fue posible abrir la URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
  Warning: unable to access index for repository http://bioconductor.org/packages/3.0/data/annotation/bin/macosx/el-capitan/contrib/3.5:
  no fue posible abrir la URL 'http://bioconductor.org/packages/3.0/data/annotation/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
  Warning: unable to access index for repository http://bioconductor.org/packages/3.0/data/experiment/bin/macosx/el-capitan/contrib/3.5:
  no fue posible abrir la URL 'http://bioconductor.org/packages/3.0/data/experiment/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
  Warning: unable to access index for repository http://bioconductor.org/packages/3.0/extra/bin/macosx/el-capitan/contrib/3.5:
  no fue posible abrir la URL 'http://bioconductor.org/packages/3.0/extra/bin/macosx/el-capitan/contrib/3.5/PACKAGES'_

I don't know if these warnings are important. Anyway, the program continues to execute and then jumps to the next error, which is the installation of BiocGenerics. I manually downloaded the tar.gz and skipped the error, but then another appeared.

_Installing Rcpp (0.11.6) ...
[1]
"Command failed (1)\n\nFailed to run system command:\n\n\t'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL '/private/var/folders/3q/skwv9bz16r3gc91k9ycdzq6h0000gn/T/RtmpGpOjnz/Rcpp' --library='/Users/alex/Desktop/R/Software/DECoN-master/Linux/packrat/lib/x86_64-apple-darwin15.6.0/3.5.1' --install-tests --no-docs --no-multiarch --no-demo \n\nThe command failed with output:\n* installing source package 'Rcpp' ...\n** package 'Rcpp' successfully unpacked and MD5 sums checked\n** libs\nclang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fPIC -Wall -g -O2 -c Date.cpp -o Date.o\nIn file included from Date.cpp:31:\nIn file included from ../inst/include/Rcpp.h:73:\n../inst/include/Rcpp/Rmath.h:222:55: error: no member named 'Rf_pythag' in the global namespace; did you mean 'pythag'?\n inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }\n ^~~~~~~~~~~\n pythag\n../inst/include/Rcpp/Rmath.h:222:19: note: 'pythag' declared here\n inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }\n ^\n1 error generated.\nmake: *** [Date.o] Error 1\nERROR: compilation failed for package 'Rcpp'\n* removing '/Users/alex/Desktop/R/Software/DECoN-master/Linux/packrat/lib/x86_64-apple-darwin15.6.0/3.5.1/Rcpp'"
Error: Command failed (1)

Failed to run system command:

'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL '/private/var/folders/3q/skwv9bz16r3gc91k9ycdzq6h0000gn/T/RtmpGpOjnz/Rcpp' --library='/Users/alex/Desktop/R/Software/DECoN-master/Linux/packrat/lib/x86_64-apple-darwin15.6.0/3.5.1' --install-tests --no-docs --no-multiarch --no-demo 

The command failed with output:

• installing source package 'Rcpp' ...
  ** package 'Rcpp' successfully unpacked and MD5 sums checked
  ** libs
  clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fPIC -Wall -g -O2 -c Date.cpp -o Date.o
  In file included from Date.cpp:31:
  In file included from ../inst/include/Rcpp.h:73:
  ../inst/include/Rcpp/Rmath.h:222:55: error: no member named 'Rf_pythag' in the global namespace; did you mean 'pythag'?
  inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }

Además: Warning message:
In packrat::restore() :
The most recent snapshot was generated using R version 3.1.2_

I am now stuck here and cannot find a solution browsing on the internet. Anyone has any ideas? I would very much like to be able to use DECoN.

Thanks in advance.

Installation of DECoN failed

Hello, I am trying to install DECoN V2 but I have some issues.

It seems it can't install the package ExomeDepth (error message below from the setup.log file).
I tried to install ExomeDepth from github (install_github("vplagnol/ExomeDepth")) but the installation of ExomeDepth also failed.

Does anyone encounter this issue? Is there another way to install ExomeDepth?

Thank you in advance.

[...]
Installing ExomeDepth [1.1.15] ...
        FAILED
Error installing package 'ExomeDepth':
======================================

* installing *source* package 'ExomeDepth' ...
** package 'ExomeDepth' successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-wSz8CH/r-base-4.2.1=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-str
ong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c CNV_estimate.cpp -o CNV_estimate.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-wSz8CH/r-base-4.2.1=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ExomeDepth_init.c -o ExomeDepth_init.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-wSz8CH/r-base-4.2.1=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c VP_gamma.c -o VP_gamma.o
In file included from gsl_math.h:22,
                 from VP_gamma.c:23:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ';' before 'extern'
   85 | __MATHCALL_VEC (acosh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ';' before 'extern'
   87 | __MATHCALL_VEC (asinh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ';' before 'extern'
   89 | __MATHCALL_VEC (atanh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ';' before 'extern'
  119 | __MATHCALL_VEC (expm1,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ';' before 'extern'
  122 | __MATHCALL_VEC (log1p,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ';' before 'extern'
  147 | __MATHCALL_VEC (hypot,, (_Mdouble_ __x, _Mdouble_ __y));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ';' before 'extern'
   85 | __MATHCALL_VEC (acosh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ';' before 'extern'
   87 | __MATHCALL_VEC (asinh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ';' before 'extern'
   89 | __MATHCALL_VEC (atanh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ';' before 'extern'
  119 | __MATHCALL_VEC (expm1,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ';' before 'extern'
  122 | __MATHCALL_VEC (log1p,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ';' before 'extern'
  147 | __MATHCALL_VEC (hypot,, (_Mdouble_ __x, _Mdouble_ __y));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ';' before 'extern'
   85 | __MATHCALL_VEC (acosh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ';' before 'extern'
   87 | __MATHCALL_VEC (asinh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ';' before 'extern'
   89 | __MATHCALL_VEC (atanh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ';' before 'extern'
  119 | __MATHCALL_VEC (expm1,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ';' before 'extern'
  122 | __MATHCALL_VEC (log1p,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ';' before 'extern'
  147 | __MATHCALL_VEC (hypot,, (_Mdouble_ __x, _Mdouble_ __y));
      | ^~~~~~~~~~~~~~
make: *** [/usr/lib/R/etc/Makeconf:168: VP_gamma.o] Error 1
ERROR: compilation failed for package 'ExomeDepth'
* removing '/DECoN/Linux/renv/staging/1/ExomeDepth'
Error: install of package 'ExomeDepth' failed [error code 1]
In addition: There were 12 warnings (use warnings() to see them)
Traceback (most recent calls last):
12: renv::restore()
11: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
10: renv_install_impl(records)
 9: renv_install_staged(records)
 8: renv_install_default(records)
 7: handler(package, renv_install_package(record))
 6: renv_install_package(record)
 5: withCallingHandlers(renv_install_package_impl(record), error = function(e) {
        vwritef("\tFAILED")
        writef(e$output)
    })
 4: renv_install_package_impl(record)
 3: r_cmd_install(package, path)
 2: r_exec_error(package, output, "install", status)
 1: stop(error)
Execution halted

Error when running makeCNVcalls.R

Hi,
I'm using DECoN v1.0.1 on Ubuntu 16.04

I can get DECoN to work for one of my sets of data, but for another set I keep getting the error below during the makeCNVcalls.R step.

[1] "Processing sample: 201_S6 7/7"
Optimization of the choice of aggregate reference set, this process can take some time
Number of selected bins: 63
Now fitting the beta-binomial model on a data frame with 82 rows : this step can take a few minutes.
Now computing the likelihood for the different copy number states
Correlation between reference and tests count is 0.98512
To get meaningful result, this correlation should really be above 0.97. If this is not the case, consider the output of ExomeDepth as less reliable (i.e. most likely a high false positive rate)
Number of calls for chromosome chr7 : 1
Error in Summary.factor(45:53, na.rm = FALSE) : 
  ‘min’ not meaningful for factors
Calls: unlist -> lapply -> FUN -> Summary.factor
Execution halted

Edit: I think the problem was my custom numbering file had numbers in the following format #.#.#
Is there any way to have the custom numbering column be string based and sort on the coordinates instead of the exon#? I was using #.#.# to try and force a stringish name to an exon where the design has multiple tiles across an exon and there are alternate exons (exon#.tile#.alt#)

Error with CNVcalls

Dear All,

I try to call CNV-s from a set of 5 samples.
I was able to generate RData file without difficulty. However during CNVcall I get the following error message:

Error in 1:nrow(brca) : argument of length 0
Execution halted

What could cause this issue?
Thank you
Peter

How to select meaningful CNVs?

Hey,
After many pains I've successfully run DECoN on 208 WES samples. For each sample I've got like 300-1000 CNV. Most of them are them are rubbish. Is there any hint how should I filter the last cnv.calls_plot DF in order to refine the results?

     ID     sample correlation N.comp start.p end.p        type nexons     start       end chromosome                       id    BF reads.expected reads.observed reads.ratio     Gene start.b end.b  chr
1     1 s1   0.9927666     13       1     1    deletion      1     69037     70008          1         chr1:69037-70008  2.66            309            216       0.699    OR4F5       1     1 chr1
2     2 s1   0.9927666     13     380   380 duplication      1   1645126   1645262          1     chr1:1645126-1645262  3.25            193            263       1.360   CDK11B      11    11 chr1
3     3 s1   0.9927666     13     665   665 duplication      1   3469433   3469593          1     chr1:3469433-3469593  2.69            145            197       1.360 ARHGEF16       5     5 chr1
4     4 s1   0.9927666     13    1842  1843    deletion      2  12917693  12920413          1   chr1:12917693-12920413 28.60            936            584       0.624  PRAMEF7       1     2 chr1
5     5 s1   0.9927666     13    1846  1848    deletion      3  13049808  13053659          1   chr1:13049808-13053659 33.00           1679            995       0.593 PRAMEF27       1     3 chr1
6     6 s1   0.9927666     13    1851  1852 duplication      3  13175281  13198906          1   chr1:13175281-13198906 66.20           1019           2081       2.040  PRAMEF9       1     2 chr1
6.1   6 s1   0.9927666     13    1853  1853 duplication      3  13175281  13198906          1   chr1:13175281-13198906 66.20           1019           2081       2.040 PRAMEF13       1     1 chr1
7     7 s1   0.9927666     13    1856  1856    deletion      1  13260222  13260803          1   chr1:13260222-13260803 18.60            321            136       0.424  PRAMEF5       1     1 chr1
8     8 s1   0.9927666     13    2208  2208    deletion      1  16575157  16575229          1   chr1:16575157-16575229  4.29            440            300       0.682    NBPF1       4     4 chr1
9     9 s1   0.9927666     13    2217  2217    deletion      1  16587050  16587261          1   chr1:16587050-16587261 15.30            640            350       0.547    NBPF1      13    13 chr1
10   10 s1   0.9927666     13    2219  2221    deletion      3  16588849  16592021          1   chr1:16588849-16592021  8.34           1302            933       0.717    NBPF1      15    17 chr1
11   11 s1   0.9927666     13    2865  2865 duplication      1  21480051  21480223          1   chr1:21480051-21480223  8.55            225            354       1.570    NBPF3      10    10 chr1
12   12 s1   0.9927666     13    2865  2867    deletion      2  21480051  21481769          1   chr1:21480051-21481769  5.79            752            610       0.811    NBPF3      10    12 chr1
13   13 s1   0.9927666     13    3042  3042    deletion      1  22003003  22003088          1   chr1:22003003-22003088  5.81            169             98       0.580   CELA3A       2     2 chr1
14   14 s1   0.9927666     13    5325  5325 duplication      2  39763689  39763791          1   chr1:39763689-39763791  5.27            477            629       1.320     PPIE       2     2 chr1
14.1 14 s1   0.9927666     13    5326  5326 duplication      2  39763689  39763791          1   chr1:39763689-39763791  5.27            477            629       1.320    BMP8B       3     3 chr1
15   15 s1   0.9927666     13    5329  5329 duplication      1  39788152  39788485          1   chr1:39788152-39788485  2.93            442            574       1.300    BMP8B       1     1 chr1
16   16 s1   0.9927666     13    8814  8814    deletion      1  89010904  89011116          1   chr1:89010904-89011116  3.95            257            170       0.661     GBP3       4     4 chr1
17   17 s1   0.9927666     13    9677  9686 duplication     12 103571603 103618100          1 chr1:103571603-103618100 57.20           4654           6320       1.360    AMY2B       1    10 chr1
17.1 17 s1   0.9927666     13    9687  9688 duplication     12 103571603 103618100          1 chr1:103571603-103618100 57.20           4654           6320       1.360    AMY2A       1     2 chr1

I guess I don't need to provide 200 samples or more to get higher resolution, as DECoN takes only small subset of references? (like 13 on below picture)?

Error in makeCNVcall.R - undefined columns selected

Hello,

makeCNVcalls.log

I´m getting error during the makeCNVcalls step. Any ideas what could be the cause or how to solve it?
Log attached.

Thanks a lot!

J

Installation Issue

Hi all,
Please could Someone help me with the following DECoN related problems - Sorry I am such a newbie!

I installed R3.1.2 for macosx (snow leopard), and am having trouble installing DECoN, and other required packages.

When trying to use the setup.sh script in the Linux folder, the log file showed this error:

Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
unknown timezone 'zone/tz/2021a.1.0/zoneinfo/Europe/Dublin'

• installing source package ‘packrat’ ...
  ** package ‘packrat’ successfully unpacked and MD5 sums checked
  ** R
  ** inst
  ** preparing package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
• DONE (packrat)
  Warning: unable to access index for repository http://cran.rstudio.com/bin/macosx/contrib/3.1
  Installing BiocGenerics (0.12.1) ... OK (downloaded binary)
  Installing DBI (0.3.1) ... Error in installPkg(pkgRecord, project, availablePkgs, repos, lib, cache) :
  Failed to install DBI (0.3.1): sources missing at /Users/clara/projects/cnv_analysis/DECoN-1.0.2/Linux/packrat/src/DBI/DBI_0.3.1.tar.gz
  Calls: -> restoreImpl -> playActions -> installPkg
  Execution halted

I’m also finding it difficult to identify a good repository to link to when installing required packages. For example devtools, comes with the same error regardless of the repository I try:

Warning: unable to access index for repository https://cran.ma.imperial.ac.uk/bin/macosx/contrib/3.1
Warning message:
package ‘devtools’ is not available (for R version 3.1.2)

install.packages("devtools")
Warning: unable to access index for repository https://cran.ma.imperial.ac.uk/bin/macosx/contrib/3.1
Warning message:
package ‘devtools’ is not available (for R version 3.1.2)
install.packages("devtools", repo='https://cran.r-project.org')
Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/contrib/3.1
Warning message:
package ‘devtools’ is not available (for R version 3.1.2)

Any help would be much appreciated! Thank you
Clara

DECoN v2.0.1 installation error, Rscript error and question.

I was trying to use DECoN for my target panel CNV analysis.
It had lots of error.
Thanks to wcarre, fishcakess and emunte in #40, #41 and #44, these issues helped me a lot.
In order to help other when they using DECoN V2.0.1 first time.
I would like to record the steps I took to fix these errors.

1. Installation

I downloaded the R 4.2.0 from CRAN and compiled it on CentOS.
Then I clone DECoN and run the setup.sh as Documentation said.

• version control error

But in setup.log, I got a error message.

The error was from the full version control, and there isn't old version package in CRAN.
As #41 describe, I needed to modify the version control file which is named renv.lock.
(For Windows should be same as linux, but I didn' t try it. If it was wrong, please write commen blow.)
path of renv.lock : /DECoN/Linux/renv.lock or /DECoN/Windows/renv.lock
Change the line 118 "Version": "1.1.15" to "Version": "1.1.16".

After re-running the setup.sh, the installation log showed it installed successfully.

2. Running with test datafiles

• Running orignial R scripts

The R scripts need to be run under the path of DECoN
Next, I tried to run the DECoN with DECoN .

1. ReadInBams.R
   Command :
   cd $DECoN_path
$Rscript_path ReadInBams.R --bams $rawdata_path --bed $rawdata_path/test_Target_Regions.bed --fasta $reference_path --out $output_path/1.ReadInBAM/test
   And got [1] "END ReadInBams.R" on screen.

2. IndentifyFailures.R
   Command :
   cd $DECoN_path
$Rscript_path IdentifyFailures.R **--RData** $output_path/1.ReadInBAM/test.RData --exons rawdata_path/test_customNumbering.txt --mincorr .98 --mincov 100 --custom TRUE --out $output_path/2.IdentifyFailures/testFailures
   Here the option of Summary RData file, should be --RData not the --Rdata which is describe in both Document and README in test datafiles.
   And you should got [1] "END IdentifyFailures.R" on screen.

3. makeCNVcall.R
   Command :
   cd $DECoN_path
$Rscript_path makeCNVcalls.R --RData $output_path/1.ReadInBAM/test.RData --exons $rawdata_path/test_customNumbering.txt --custom TRUE --out $output_path/3.makeCNVcalls/testCalls --plot All --plotFolder $output_path/3.makeCNVcalls/testPlots
   Remeber, the option of Summary RData file is same as IndentifyFailures.
   Should be --RData not the --Rdata.
   After that you got [1] "END makeCNVCalls.R".

But when I checked the "testCalls_custom.txt", it was totally differnet from the README in test datafiles.

As the README, should only be a sample 207 BRCA1 deletion.

• Corrected the IndentifyFailures.R and makeCNVcall.R

Thank for wcarre, fishcakess corrected the bug in IndentifyFailures.R and makeCNVcall.R.
I corrected the colnames(ExomeCount)[1:length(sample.names)+4]=sample.names to colnames(ExomeCount)[1:length(sample.names)+5]=sample.names
For IndentifyFailures.R, change colnames(ExomeCount)[1:length(sample.names)+4]=sample.names to colnames(ExomeCount)[1:length(sample.names)+5]=sample.names in line 57.
For makeCNVcall.R, change colnames(ExomeCount)[1:length(sample.names)+4]=sample.names to colnames(ExomeCount)[1:length(sample.names)+5]=sample.names in line 69.
And re-run all command above.
Finally, I got the results as same as the README.


Hope this page can help others who getting to use this package.

3. Question

Lastly, I have a question about my analysis. I have around 900 target panel NGS data.
They are from the same panel but different batches. And they can be categorized into two main groups: normal group (may contain some unknown CNV) and known CNV group.

My first question is what analysis strategy should I use?
Analyze them in a single run or analyze them separately?
My second question is some of the interesting genes are on the X chromosome. For this scenario, should I separate the samples by sex and analyze them separately?

Error when running makeCNVCalls with ~ 400 Samples

Hi,

I try to run DECoN with around 400 samples at once. ReadInBams take a long time to run but end without any errors. When I try to run make makeCNVCalls it exits with:

Error in `colnames<-`(`*tmp*`, value = c("space", "start", "end", "width",  : 
  'names' attribute [374] must be the same length as the vector [372]
Execution halted

With around 80 samples all parts are running smoothly.

Thank you in advance!

DECoN packages management

Dear all,
thanks to #45 I was able to install DECoN on my machine and I also tried the tool in two different runs.
I created a conda enviroment with the correct R version and all the packages required.
The problem is when I close the enviroment and I log off from the machine.
When I log in again in the machine and I activate the enviroment, the tool ask me to install all the dependencies again.
I think it is a renv problem but I am not understanding what is the problem.
Could someone help me?

Thanks in advance,

Error encountered while executing IdentifyFailures.R

command

Rscript /home/bioinfo/RahmanTeam-DECoN-8d740c5/Linux/IdentifyFailures.R --Rdata output.prefix.RData --mincorr .98 --mincov 100 --custom FALSE

output

[1] "BEGIN IdentifyFailures.R"
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following objects are masked from ‘package:methods’:

    getClasses, getMethods

The following objects are masked from ‘package:base’:

    attach, detach, gc, load, save

R.utils v2.6.0 (2017-11-04) successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

    timestamp

The following objects are masked from ‘package:base’:

    cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
    warnings

Error in `$<-.data.frame`(`*tmp*`, chromosome, value = character(0)) : 
  replacement has 0 rows, data has 219286
Calls: $<- -> $<-.data.frame
Execution halted

failed installation

Hi my DECoN installation fails in Ubuntu. Below the output of setup.log:

Please help

`* installing source package ‘packrat’ ...
** package ‘packrat’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

• DONE (packrat)
  Installing BiocGenerics (0.12.1) ... OK (built source)
  Installing DBI (0.3.1) ... OK (built source)
  Installing R.methodsS3 (1.7.0) ... OK (built source)
  Installing R6 (2.0.1) ... OK (built source)
  Installing RColorBrewer (1.1-2) ... OK (built source)
  Installing RJSONIO (1.3-0) ... OK (built source)
  Installing Rcpp (0.11.6) ... [1] "Command failed (1)\n\nFailed to run system command:\n\n\t'/usr/lib/R/bin/R' --vanilla CMD INSTALL '/tmp/Rtmp2tJxun/Rcpp' --library='/home/faber/BioIT/tools/DECoN-1.0.1/Linux/packrat/lib/x86_64-pc-linux-gnu/3.6.3' --install-tests --no-docs --no-multiarch --no-demo \n\nThe command failed with output:\n* installing source package 'Rcpp' ...\n** package 'Rcpp' successfully unpacked and MD5 sums checked\n** using staged installation\n** libs\ng++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o\nIn file included from ../inst/include/Rcpp/Module.h:335:0,\n from ../inst/include/Rcpp.h:64,\n from Date.cpp:31:\n../inst/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]\n void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){\n ^~~~~\n../inst/include/Rcpp/module/Module_Property.h:161:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]\n void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){\n ^~~~~\nIn file included from ../inst/include/Rcpp.h:73:0,\n from Date.cpp:31:\n../inst/include/Rcpp/Rmath.h: In function 'double R::pythag(double, double)':\n../inst/include/Rcpp/Rmath.h:222:57: error: '::Rf_pythag' has not been declared\n inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }\n ^~~~~~~~~\n../inst/include/Rcpp/Rmath.h:222:57: note: suggested alternative: 'pythag'\n inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }\n ^~~~~~~~~\n pythag\n/usr/lib/R/etc/Makeconf:177: recipe for target 'Date.o' failed\nmake: *** [Date.o] Error 1\nERROR: compilation failed for package 'Rcpp'\n* removing '/home/faber/BioIT/tools/DECoN-1.0.1/Linux/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp'"
  Error: Command failed (1)

Failed to run system command:

'/usr/lib/R/bin/R' --vanilla CMD INSTALL '/tmp/Rtmp2tJxun/Rcpp' --library='/home/faber/BioIT/tools/DECoN-1.0.1/Linux/packrat/lib/x86_64-pc-linux-gnu/3.6.3' --install-tests --no-docs --no-multiarch --no-demo 

The command failed with output:

• installing source package 'Rcpp' ...
  ** package 'Rcpp' successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o
  In file included from ../inst/include/Rcpp/Module.h:335:0,
  from ../inst/include/Rcpp.h:64,
  from Date.cpp:31:
  ../inst/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  void set(Class* obj
  In addition: There were 15 warnings (use warnings() to see them)
  Execution halted
  `

Rsamtools version not compatible with VN:1.4 BAM files?

Dear, I would really like to test DECoN. The installation was successful, but I get following error message when I try to run ReadInBams.R with our BAM files:

Error in value[[3L]](cond) : 
  failed to open BamFile: SAM/BAM header missing or empty
  file: 'file.bam'
Calls: getBamCounts ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_header_read] invalid BAM binary header (this is not a BAM file).
Execution halted

According the error message, the headers are missing, but they are not! The upper header lines of my BAM files look like this:

@HD	VN:1.4	SO:coordinate
@SQ	SN:chr1	LN:248956422
@SQ	SN:chr2	LN:242193529
@SQ	SN:chr3	LN:198295559
@SQ	SN:chr4	LN:190214555
@SQ	SN:chr5	LN:181538259
@SQ	SN:chr6	LN:170805979
@SQ	SN:chr7	LN:159345973
@SQ	SN:chr8	LN:145138636
...

I seems to me that the error message is made by the Rsamtools package version 1.18.3. If I read my BAM file with a more recent Rsamtools version (eg. v2.8.0), I do not get this message. But as DECoN depends on an old R version (3.1.2), it's not just possibly to use a more recent Rsamtools version (and all it's dependencies). Does anyone know an easy (or less easy) fix for this issue?

Differences between V1 and V2

Dear Developers,
In our lab we introduce DECoN to identify putative CNV for samples enriched and sequenced with illumina TruSight Cancer kit.
Recently we installed in our server, the V2 and yesterday I tried the new version in previously analysed runs.
Surprisingly, I obtained different results, despite the fact that genome version and bed used are the same.
Can you please describe me the differences between the two version?
Are there tests that I can perform in order to evaluate which results are more reliable?
Moreover, the documentation has an error: is indicated the option --Rdata while the correct one is --RData.

Thanks in advance,

Error in if (MaxCorr[i] < corr_thresh) { : missing value where TRUE/FALSE needed

Rscript IdentifyFailures.R --RData=../../testdedup.RData --mincorr=.98 --mincov=30 --out=../../test82

• The library is already synchronized with the lockfile.
  [1] "BEGIN IdentifyFailures.R"
  Loading required package: R.oo
  Loading required package: R.methodsS3
  R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following object is masked from ‘package:R.methodsS3’:

throw

The following objects are masked from ‘package:methods’:

getClasses, getMethods

The following objects are masked from ‘package:base’:

attach, detach, load, save

R.utils v2.11.0 (2021-09-26 08:30:02 UTC) successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

timestamp

The following objects are masked from ‘package:base’:

cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
warnings

Error in if (MaxCorr[i] < corr_thresh) { :
missing value where TRUE/FALSE needed
Execution halted

i dont know why the MaxCorr was filled by all NA!!

IdentifyFailures Error

Thanks a lot for this great tool.

I ran command "Rscript IdentifyFailures.R --RData test.RData --mincorr .98 --mincov 100 --exons target_bed_exon.txt --out test", and error as following message,

• The library is already synchronized with the lockfile.
  [1] "BEGIN IdentifyFailures.R"
  Loading required package: R.oo
  Loading required package: R.methodsS3
  R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.25.0 (2022-06-12 02:20:02 UTC) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following object is masked from ‘package:R.methodsS3’:

throw

The following objects are masked from ‘package:methods’:

getClasses, getMethods

The following objects are masked from ‘package:base’:

attach, detach, load, save

R.utils v2.12.0 (2022-06-28 03:20:05 UTC) successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

timestamp

The following objects are masked from ‘package:base’:

cat, commandArgs, getOption, isOpen, nullfile, parse, warnings

Error in cor(ReadDepths) : supply both 'x' and 'y' or a matrix-like 'x'
Execution halted

Thanks a lot.

Problem installing DECoN

I am on windows 10 machine and I can't install DECoN 1.0.2. When I run the setup.bat script nothing happens. I get a message but it nothing actually runs.

I have the recommended version of Rtools installed and in the right path and I run the script as an admin (from both GUI and command line, same result).

Error in ReadInBams.R GenomicRanges::seqnames(target)

Hello,

I tried to use ReadInBams.R command in Linux to generate the first file. However, I got an error as follows:

Error in GenomicRanges::seqnames(target) : object 'target' not found
Calls: getBamCounts ... countBamInGRanges.exomeDepth -> paste0 ->
In addition: Warning message:
In countBamInGRanges.exomeDepth(bam.file = bam, index = index, granges = target, :
Apparently the BAM file uses the convention chr1 instead of 1 for chromosome names, but your target sequence does not. Therefore, adding the chr prefix to the target intervals
Execution halted

I am unable to find a way to remove "chr" convention from BAM files. Can you help please?

Thanks!

samples off by one

Using the latest version of decon I'm getting a consistent error.
The first bam file is always described in the Failures.txt file as:
All Whole sample All Low correlation: 0.29554106282364, Low median read depth (FPKM): 0.405555555555556
In addition the CNV calls are always off by one so known CNVs are assigned to the incorrect sample.
Any help would be appreciated.
Andrew