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ChrisMaherLab / SV-Hotspot

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Error: The annotation file does not exits!. #6

Open yangsui0122 opened 1 month ago

yangsui0122 commented 1 month ago

Hi, I tried to run your test_data, but I got this error:

########################################################
######             SV-HotSpot v1.0.0              ######
########################################################
 SVs file              : modules-sw/sv-hotspot/691fa23/Linux/Ubuntu22.04/x86_64/test_data/sv.bedpe
 Genome name           : hg38
 Sliding window size   : 100000
 Sliding window step   : 30000
 Output directory      : OUTPUT/sv-hotspot-output
 Annotation file       : annotations/hg38/genes.bed
 peakPick window size  : 100
 peakPick minimum SD   : 5
 % of samples cutoff   : 10
 Expression file       : modules-sw/sv-hotspot/691fa23/Linux/Ubuntu22.04/x86_64/test_data/exp.tsv
 Copy number file      :modules-sw/sv-hotspot/691fa23/Linux/Ubuntu22.04/x86_64/test_data/cna.tsv
 Amplification cutoff  : 2.99
 Deletion cutoff       : 1.35
 Genes of interest     : 0
 Region of interest    : modules-sw/sv-hotspot/691fa23/Linux/Ubuntu22.04/x86_64/test_data/enhancers.bed
 Chromosomes to analyze: chrX
 SV types to analyze   : ALL
 Peak merge distance   : 50000
 Number of nearby genes: 1
 ChIP-Seq cov. file    : modules-sw/sv-hotspot/691fa23/Linux/Ubuntu22.04/x86_64/test_data/H3K27ac.bg
 Statistical test      : wilcox.test
 Plot top peaks        : 10
 ChIP-seq coverage     : H3K27ac
 Left extension size   : 100000
 Right extension size  : 100000
 % of samples to merge : 5
 # of stop-merge peaks : 0
########################################################

--------------------------------------------------
Input Verification Step
--------------------------------------------------
Checking structural variants file format...PASS.

 Error: The annotation file does not exits!.

I can see the genes.bed in the annotation folder, and in the manual:

Optional files:
An annotation file in [BED](https://genome.ucsc.edu/FAQ/FAQformat.html) format. If the user didn't provide this file, a built-in annotation file based on the genome name will be used. Please note that the feature in the expression file has to match the one in this file.

May I ask how I can fix this? Thanks.

Eteleeb commented 1 month ago

Hi, Thank you for using our tool. Looks like you are not providing the right path to the annotation file. Are you running it as a docker image or using the original script?. Anyway, the easiest and quick solution is to provide the file using -a/--annot and the file from the annotation folder.

Let me know if this didn't work.

Abdallah