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ulelab / iCount-Mini

iCount, protein-RNA interaction analytics
http://icount.biolab.si
MIT License
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Help understanding why 'iCount-Mini peaks' freezes #4

Open valerieT1998 opened 1 year ago

valerieT1998 commented 1 year ago

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 commented 1 year ago

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