medvedevgroup / cnfind Goto Github PK

(from Rayan)

(culprit: the following line in cnfind: my $Rfolder = File::HomeDir->my_home . "/bin/";)

-> Put in the README that Rscript should be linked to ~/bin/Rscript
or find a way for perl to automatically find Rscript

(from Rayan)

command failed: 2File [work_dir]/mapping_files/chr1.rmap does not exist!

That means cnfind is not compiled :) type make in the cnfind folder..

(Email from Chen)
The error messages are as follows:

Exec at 14:55:56, Fri Apr 25, 2014 /gpfs/home/cxs1031/bin//Rscript /gpfs/home/cxs1031/src/cnfind/segment.R 0 0.05  /gpfs/home/cxs1031/backup/data/cnfind_0424/chr1/chr1.win.forsegme
nt /gpfs/home/cxs1031/backup/data/cnfind_0424/chr1/chr1.segments chr1 lrOsEs 0 1000000 0...
Error in sort(abs(diff(genomdat)))[1:n.keep] : 
  only 0's may be mixed with negative subscripts
Calls: smooth.CNA -> trimmed.variance
Execution halted
Exec at 14:56:5, Fri Apr 25, 2014 /gpfs/home/cxs1031/bin//Rscript /gpfs/home/cxs1031/src/cnfind/plot_doc.R chr1 1008 /tmp/ONJjOIaWcg/chr1.covplot nosnps /gpfs/home/cxs1031/backup/d
ata/cnfind_0424/chr1/chr1.segments 0 nocalls nocalls lrOsEs /gpfs/home/cxs1031/backup/data/cnfind_0424/chr1/chr1.win Sample black 
...
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/gpfs/home/cxs1031/backup/data/cnfind_0424/chr1/chr1.segments': No such file or directory
Execution halted

The error point directly to file segment.R, line 36. And the reason is because I did not provide mapping information for chromosome 1. So the matrix parameter of function smooth.CNA is null or all 0, which is illegal. We can check whether there is information for a specific chromosome before deal with it, or we can provide a parameter to specify certain chromosomes at the very beginning of pipeline.

The similar error happens to file plot_doc.R.

Genome-wide analysis including chr1-22 plus chrX, but there is not chrY

When running with a new version of R, you get
“Fatal error: you must specify '--save', '--no-save' or '--vanilla'

The fix for this is to change the way Rscript is called, at every instance. For example, the line that calls "doc_walker" must be changed to

execCommand("cat $win_file.1 | $exec_folder/doc_walker $scov_file $exp_file full | $exec_folder/gcContent $ref_folder/fasta_files_folder/$chr.fa | $Rfolder/Rscript --slave --file=$exec_folder/annot1_win.R \"--args $win_file.2\" ", $par);

(from Rayan)

`perl cnfind.pl` crashes with: "Can't locate File/HomeDir.pm in @INC .."

Need to install File::HomeDir in Perl.

To do this, type this in a terminal (no root needed):

wget -O- http://cpanmin.us | perl - -l ~/perl5 App::cpanminus local::lib
eval perl -I ~/perl5/lib/perl5 -Mlocal::lib
echo 'eval perl -I ~/perl5/lib/perl5 -Mlocal::lib' >> ~/.bash_profile
cpanm File::HomeDir
restart bash

(follows http://stackoverflow.com/questions/2980297/how-can-i-use-cpan-as-a-non-root-user)

Currently, the MAKE_WIN stage runs make_masked_win to divide the genome up into windows with a given target size. We should allow the user to generate their own window files and pass them to cnfind.pl. When this option is invoked, cnfind should check that the windows are "proper" (non-overlapping, and within the bounds of the chromosome lengths defined in the companion package.

(from Rayan)

make_simple_coverage crashed with "Error, out of range position 198102932 on ref chr3 of size 198022430." (to reproduce: gbm_7_t bam file on hg19)

Means that the BAM file was created with another reference. One should find and use the correct reference (hg19 or hg18 or other, but no companion package for others).

Convert the calls file to a vcf file at the last step

DNAcopy is absent from the prerequisites in README

-> these commands need to be typed in R to install DNACopy:

source("http://bioconductor.org/biocLite.R")

biocLite("DNAcopy")

update README with this info