Error message when running atlas - sample file format ?

[luckyluke95]

Dear authors,

I want to use your software to call CNV in a targeted-gene panel.
But I have a problem when I execute this command to run the atlas_cnv.pl script :

perl ./atlas_cnv.pl --config PATHtoCONFIG/atlas_cnv.config --panel PATHtoPANELfile/panel_neuro_file_atlas_cnv.txt --sample PATHtoPANElsample/atlas_cnv.sample

I have the following message :

Error in file(file, "rt") : impossible to open the connexion
Calls: read.table -> file
More over : Warning message:
In file(file, "rt") :
  impossible to open the file 'run11/NRP278_S9.DATA.sample_interval_summary' : no such file or directory
Execution stopped

I can join you my files if you can help me :... zipped.zip

I really do not understand what can be wrong... maybe I misunderstand what is the "midpool" in the sample file ?

Thanks in advance for yout help

Abou

[luckyluke95]

I forgot
At the end of the error message, I have this also :

Error in `[<-.data.frame`(`*tmp*`, a, i, value = NA) : 
  replacement has 1 row, data has 0
Calls: remove_5pc_outliers -> [<- -> [<-.data.frame
Execution stopped
mkdir: impossible to create the directory «Sample_S9/CNV»: No such file or directory
cp: impossible d'évaluer 'run11/NRP278_S9.cnv*': No such file or directory
cp: impossible d'évaluer 'run11/NRP278_S9.pdf': No such file or directory

[theodorc]

zipped_fixed.zip
Hi luckyluke95,

Thank you for your interest in Atlas-CNV.

1. The coverage filenames should include the 'DATA' in the file suffix: '.sample_interval_summary' such as: NRP278_S9.DATA.sample_interval_summary

2. The panel file and the *DATA.sample.interval_summary files should be sorted by chromosome with consistent format. You had '1:10000' in the panel file, and 'chr1:10000' in the DATA.sample.interval_summary file. The panel file was also not sorted by chr.

3. GATK reports 1-based bed files, so the GATK output will have start positions which are +1 compared to your input bed file. So you can either +1 to the starts in your panel file or -1 to the starts in the -L interval files you give GATK. Basically the coordinates in the GATK DoC file should be identical to the --panel .

4. config file needs to have the [SAMPLE_FCLBC] in the GATKDIR field.

I made fixes and changes in the attached zipped fixed file that reflect above.

-Best
Ted

[luckyluke95]

Hi Ted,

Thank you very much.
It works fine with your corrections.
These datas can now be used by everyone as examples ;-)

I am happy to be able to use your tool.
Thanks again for your reactivity and helpfoolness

Abou