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mrmosaic's Issues

R version for the tool

Hey, does mr.mosaic require a particular R version or R version after certain release? I am asking because when I tried to make the code, got the following error:

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace ‘proto’ 0.3-10 is already loaded, but >= 1.0.0 is required

How to run cnv_baf_data

Hi,

I am trying to install & run MrMosaic with Docker. My Dockerfile to install mrmosaic looks like this:

FROM biocontainers/biocontainers:v1.0.0_cv4

RUN apt-get update && \
    apt-get -y install gcc make vim libssl-dev libncurses-dev

RUN conda install r-base=3.4.3

RUN Rscript -e "install.packages('gada', repos='http://R-Forge.R-project.org')" && \
    Rscript -e "install.packages('openssl',repos='http://cran.us.r-project.org')" && \
    Rscript -e "install.packages('devtools',repos='http://cran.us.r-project.org')" && \
    Rscript -e "install.packages('yaml',repos='http://cran.us.r-project.org')" && \
    Rscript -e "install.packages('argparse',repos='http://cran.us.r-project.org')" && \
    Rscript -e "install.packages('zoo',repos='http://cran.us.r-project.org')"

RUN F77=gfortran && \
    FC=gfortran && \
    FLIBS="-L/Users/as33/homebrew/lib/gcc/5 -lgfortran -lquadmath -lm"

RUN cd /data && \
    wget https://github.com/asifrim/mrmosaic/archive/master.zip && \
    unzip master.zip && \
    cd mrmosaic-master
    # make

I also had to make the following modifications for the installation to work before running make as recommended by @dwalinybalin:

  • mv mrmosaic/R/plot_* mrmosaic/scripts/
  • change the installation line in install_package.R to install.packages("mrmosaic", repos=NULL, type="source")

After building the image, running all of the commands & making the changes from above I had successfully installed MrMosaic

I then compiled the c file:

gcc -O3 -Wall -Isrc -I. -Ihtslib-1.3/ -Ihtslib-1.3/htslib -rdynamic -o cnv_baf_data -Lhtslib-1.3/ -L. cnv_baf_data.c -lhts -lbam -lpthread -lz -lm

Now if I try running the file:

./bin/cnv_baf_data -R ./resources/cnv_baf_bait_region_file.txt aln_new.bam aln_new.mrm

I get a Segmentation fault even though I have removed the chr prefix from my BAM file.

Does anyone have any ideas what the problem might be and how it can be resolved?
Many thanks in advance

I have also seen other people have had issues installing the software. Hopefully if I can install and run the software successfully via docker than this may be an easier way for others to run MrMosaic as well.

multithreading

Hi,

Is there a way to make MrMosaic multithreading.

thanks

Crash running step2

As a test I run step 2 using 5 samples as reference and the software worked fine.

When running step 2 using 124 samples as reference the script crashes telling the following:

Loading required package: proto

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

[1] "2017-10-25 19:58:49 : Calculating Log2 Ratios..."
[1] "OK1"
Error in cor(data[, 2] + 0.01, read_unique_depth_bait_data(x, nrow(data))[,  :
  incompatible dimensions
Calls: calc_log2_ratio ... generate_correlation_values -> sapply -> lapply -> FUN -> cor
Además: Warning message:
In read.table(pipe(paste("awk -F", "\"\t\"", " '!_[$1]++' ", file,  :
  line 1 appears to contain embedded nulls
Broken execution

Unable to install it in Ubuntu 16.04.1 and RHEL 7.3

Hi, my name is Marcos and I'm trying to install your caller without sucess in two different machines, one with Ubuntu 16.04.1 OS and the other machine with RHEL 7.3 OS. Both machines have R 3.3.2 installed, and gcc (5.4.0 in ubuntu and 4.8.5 in RHEL).

When installing the caller following your guidelines, I got the same problem on both machines when doing the "make":

In RHEL

Rscript install_package.R
> 
> list.of.packages <- c("devtools","argparse","yaml","zoo")
> new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
> if(length(new.packages)) install.packages(new.packages,repos="https://mirrors.ebi.ac.uk/CRAN/")
> 
> library(devtools)
> install_github("asifrim/mrmosaic",ref="master",subdir="mrmosaic")
Downloading GitHub repo asifrim/mrmosaic@master
from URL https://api.github.com/repos/asifrim/mrmosaic/zipball/master
Installing mrmosaic
'/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL  \
  '/tmp/RtmpQbj3eu/devtools4cd54aacbda3/asifrim-mrmosaic-969c39a/mrmosaic'  \
  --library='/home/genetica/R/x86_64-redhat-linux-gnu-library/3.3'  \
  --install-tests 

* installing *source* package ‘mrmosaic’ ...
** R
** preparing package for lazy loading
usage: PROGRAM [-h] [--child CHILD] [--dad DAD] [--mum MUM] [--denovo DENOVO]
               [--prefix PREFIX] [--outputdir OUTPUTDIR]
PROGRAM: error: unrecognized arguments: nextArg/tmp/RtmpQbj3eu/devtools4cd54aacbda3/asifrim-mrmosaic-969c39a/mrmosaicnextArg--library=/home/genetica/R/x86_64-redhat-linux-gnu-library/3.3nextArg--install-tests
Error: Command failed (1)
Ejecución interrumpida
make[1]: *** [install_r_package] Error 1
make[1]: se sale del directorio `/home/SHARED/Software/mrmosaic'
make: *** [default] Error 2

In Ubuntu:

Rscript install_package.R
> 
> list.of.packages <- c("devtools","argparse","yaml","zoo")
> new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
> if(length(new.packages)) install.packages(new.packages,repos="https://mirrors.ebi.ac.uk/CRAN/")
> 
> library(devtools)
> install_github("asifrim/mrmosaic",ref="master",subdir="mrmosaic")
Downloading GitHub repo asifrim/mrmosaic@master
from URL https://api.github.com/repos/asifrim/mrmosaic/zipball/master
Installing mrmosaic
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL  \
  '/tmp/Rtmpk8IHRq/devtools42bb47a2fd3/asifrim-mrmosaic-969c39a/mrmosaic'  \
  --library='/home/genetica/R/x86_64-pc-linux-gnu-library/3.3'  \
  --install-tests 

* installing *source* package ‘mrmosaic’ ...
** R
** preparing package for lazy loading
usage: PROGRAM [-h] [--child CHILD] [--dad DAD] [--mum MUM] [--denovo DENOVO]
               [--prefix PREFIX] [--outputdir OUTPUTDIR]
PROGRAM: error: unrecognized arguments: nextArg/tmp/Rtmpk8IHRq/devtools42bb47a2fd3/asifrim-mrmosaic-969c39a/mrmosaicnextArg--library=/home/genetica/R/x86_64-pc-linux-gnu-library/3.3nextArg--install-tests
Error: Command failed (1)
Execution halted
Makefile:15: recipe for target 'install_r_package' failed
make[1]: *** [install_r_package] Error 1
make[1]: Leaving directory '/home/SHARED/Software/mrmosaic'
Makefile:2: recipe for target 'default' failed
make: *** [default] Error 2

Is there any solution for those problems?

Thanks in advance,

Marcos

Make command failure

After installing the prerequisites and launching make, I am getting this error and output:

make cnv_baf_data
wget -N https://sourceforge.net/projects/samtools/files/samtools/1.3/samtools-1.3.tar.bz2
make[1]: wget: No such file or directory
make[1]: *** [cnv_baf_data] Error 1
make: *** [default] Error 2

Make failure

Hi there,
I am trying to install the mrmosaic using the below commands,

git clone https://github.com/asifrim/mrmosaic
cd mrmosaic
make

The make command fails with below error ...

> list.of.packages <- c("devtools","argparse","yaml","zoo")
> new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
> if(length(new.packages)) install.packages(new.packages,repos="https://mirrors.ebi.ac.uk/CRAN/")
>
> library(devtools)
Loading required package: usethis
> install_github("asifrim/mrmosaic",ref="master",subdir="mrmosaic")
Downloading GitHub repo asifrim/mrmosaic@master

Skipping 1 packages not available: gada
✔  checking for file ‘/tmp/RtmpJpO6Kb/remotes38f27d7cd3a1/asifrim-mrmosaic-969c39a/mrmosaic/DESCRIPTION’ (908ms)
─  preparing ‘mrmosaic’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘mrmosaic_0.1.tar.gz’

* installing *source* package ‘mrmosaic’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Error in read.table(file = file, header = header, sep = sep, quote = quote,  :
  'file' must be a character string or connection
Error: unable to load R code in package ‘mrmosaic’
Execution halted
ERROR: lazy loading failed for package ‘mrmosaic’

I am using R/4.0.2 version.

Any help to overcome the error would be much appreciated

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