Hi，
I'm trying to run your test data.
I encountered an error
########################################################
###### SV-HotSpot v1.0.0 ######
########################################################
SVs file : sv.bedpe
Genome name : hg38
Sliding window size : 100000
Sliding window step : 30000
Output directory : OUTPUT/sv-hotspot-output
Annotation file : /share/home/sunLab/lihe/biosoft/SV-Hotspot/annotations/hg38/genes.bed
peakPick window size : 100
peakPick minimum SD : 5
% of samples cutoff : 10
Expression file : exp.tsv
Copy number file : cna.tsv
Amplification cutoff : 2.99
Deletion cutoff : 1.35
Genes of interest : 0
Region of interest : enhancers.bed
Chromosomes to analyze: chrX
SV types to analyze : ALL
Peak merge distance : 50000
Number of nearby genes: 1
ChIP-Seq cov. file : 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.
Checking annotation file format...PASS.
Checking region of interest file(s) format...PASS.
Checking ChIP-Seq coverage file format...PASS.
Checking copy number file format...PASS.
Checking if the expression file has no duplicated rows...PASS.
Checking if feature name in the expression matches the one in the annotation file...PASS.
--------------------------------------------------
STEP 1: Identifying Peaks (hotspot regions)
--------------------------------------------------
Segmenting the genome into sliding windows
Chromosomes to segment:
[1] "chrX"
chrX
Overlapping breakpoints with sliding windows
Splitting the overlapped file by chromosome
Summarizing sample counts for chromosome chrX
Reading window data...
5202 unique windows were found
Summarizing...
Counting samples for "ALL" structural variants... 5202 windows reported (including windows w/o count).
Counting samples for "INV" structural variants... 5202 windows reported (including windows w/o count).
Counting samples for "BND" structural variants... 5202 windows reported (including windows w/o count).
Counting samples for "DUP" structural variants... 5202 windows reported (including windows w/o count).
Counting samples for "DEL" structural variants... 5202 windows reported (including windows w/o count).
Counting samples for "INS" structural variants... 5202 windows reported (including windows w/o count).
Call structural variant peaks (hotspots)
Reading sliding window sample count...
Chromosomes to analyze:
[1] "chrX"
chrX
Number of peaks: 153
Warning messages:
1: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
2: Removed 59 rows containing missing values (`geom_bar()`).
3: Removed 1 rows containing missing values (`geom_text()`).
--------------------------------------------------
STEP 2: Annotating Peaks
--------------------------------------------------
Can't exec "/share/home/sunLab/lihe/biosoft/SV-Hotspot/src/annotate_peaks.sh": Permission denied at /share/home/sunLab/lihe/biosoft/SV-Hotspot/src/sv-hotspot.pl line 520.
Summarizing annotated peaks...Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file 'OUTPUT/sv-hotspot-output/processed_data/peaks_overlap_bp.tsv': No such file or directory
Execution halted
------------------------------------------------------------------------------------
STEP 3: Determining the association between SVs and the expression of nearby genes
-------------------------------------------------------------------------------------
Loading required package: data.table
Reading expression data...done.
Reading all breakpoints...Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file 'OUTPUT/sv-hotspot-output/processed_data/peaks_overlap_bp.tsv': No such file or directory
Execution halted
--------------------------------------------------
STEP 4: Visualizing hotspot regions
--------------------------------------------------
cut: OUTPUT/sv-hotspot-output/annotated_peaks_summary.tsv: No such file or directory
Warning message:
NAs introduced by coercion
Warning message:
NAs introduced by coercion
Reading all breakpoints...Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning messages:
1: In file(file, "rt") :
'raw = FALSE' but 'OUTPUT/sv-hotspot-output' is not a regular file
2: In file(file, "rt") :
cannot open file 'OUTPUT/sv-hotspot-output': it is a directory
Execution halted
Hi， I'm trying to run your test data. I encountered an error
Can you help me troubleshoot? Thanks