ERROR for exome capture prob file

[jaybee84]

Hello,

I am trying to implement CN_Learn for calling copy number variants in a exome-seq dataset. But I am running into the error describe below:

> bash precheck.sh 
STATUS: PROJ_DIR path in the config.params file has been updated successfully.
STATUS: source path in all the bash scripts has been updated successfully.
STATUS: REF_GENOME file path has been updated.
STATUS: BAM_FILE_DIR file path has been updated
STATUS: Input BAM files are available for processing.
STATUS: Each bam file has a corresponding index file associated with it.
STATUS: Creating the required input files with the list of sample names.
STATUS: Creating the required input files with sample names for CANOES processing.
ERROR: The exome capture prob file is not formatted correctly. Please make 
sure that the input file is tab separated without headers.

I have been trying to troubleshoot the last ERROR message but with no success. Investigating the original files in the source dir shows:

> cd source
> head exome_capture_targets.bed
Y   150854  150981
Y   155399  155536
Y   157314  157443
Y   158165  158321
Y   159701  159885
Y   165763  166002
Y   171740  171864
Y   174026  174179
Y   174398  174547
Y   178085  178294

> head targets_auto_no_chr.bed
1   30366   30503
1   69089   70010
1   367657  368599
1   621094  622036
1   861320  861395
1   865533  865718
1   866417  866471
1   871150  871278
1   874418  874511
1   874653  874842

The paths to appropriate files have been updated in the config.params file. What am I missing?

Thanks!

[girirajanlab]

Hello Jineta, A check is in place to make sure that the input file only has probes from the autosomes. Please try again by providing only the autosome probes in the exome_capture_targets.bed file.

Vijay