Help understanding why 'iCount-Mini peaks' freezes

[valerieT1998]

Hi,

I am having some trouble running the peaks function of iCount-Mini, the process just stops and no output is generated even after 2 days of running ( no update on the log file either ). The gtf_segmentation.gtf was generated with iCount-Mini segment

Here's the content of my log ( changed the path for reading) :
"
Executing the following command: iCount peaks
/path_to/templates/output/segment/gtf_segmentation.gtf
/path_to/tollervey_SHSY5Y_nucl.xl.bed
/path_to/templates/output/peaks/peaks.bed
Input parameters for function 'run' in iCount.analysis.peaks
sites: /path_to/templates/output/segment/gtf_segmentation.gtf
sigxls: /path_to/tollervey_SHSY5Y_nucl.xl.bed
peaks: /path_to/templates/output/peaks/peaks.bed
dist: 20
slop: 3
Reading individual sites from /path_to/templates/output/segment/gtf_segmentation.gtf
Reading sigxls from /path_to/tollervey_SHSY5Y_nucl.xl.bed
Merging sigxls to form peaks
Summing sites within identified peaks
"
And after there's nothing else...

Thank you in advance for your help

[amchakra]

The iCount-Mini peaks command merges significant crosslink sites into peaks, so should take two inputs: the xlinks BED file, the sigxls BED file and give you the merged peaks BED file output.

I think this line might give a clue to the cause of the error?

sites: /path_to/templates/output/segment/gtf_segmentation.gtf