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uio-bmi / graph_peak_caller

ChIP-seq peak caller for reads mapped to a graph-based reference genome
BSD 3-Clause "New" or "Revised" License
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peaks_to_linear error #14

Open sdws1983 opened 1 year ago

sdws1983 commented 1 year ago

Hi,

I'm using graph_peak_caller for graph-based ATAC-seq analysis, I followed the tutorial for profiling and all steps worked successfully. But when I finally got the peak file and I'd like to use the peaks_to_linear command to get the linear coordinates of the peak, the following error occurred:

$ graph_peak_caller peaks_to_linear 01_max_paths.intervalcollection index/01_linear_pathv2.interval 01 01_linear_peaks.bed
2023-05-11 20:01:29,104, INFO: Converting peak 0
Traceback (most recent call last):
  File "/share/home/miniconda3/bin/graph_peak_caller", line 33, in <module>
    sys.exit(load_entry_point('graph-peak-caller', 'console_scripts', 'graph_peak_caller')())
  File "/share/home/software/graph_peak_caller/graph_peak_caller/command_line_interface.py", line 39, in main
    run_argument_parser(sys.argv[1:])
  File "/share/home/software/graph_peak_caller/graph_peak_caller/command_line_interface.py", line 679, in run_argument_parser
    args.func(args)
  File "/share/home/software/graph_peak_caller/graph_peak_caller/analysis/analysis_interface.py", line 384, in peaks_to_linear
    linear_peaks = peaks.to_approx_linear_peaks(linear_path, args.chromosome)
  File "/share/home/software/graph_peak_caller/graph_peak_caller/peakcollection.py", line 249, in to_approx_linear_peaks
    linear_peaks.append(peak.to_approx_linear_peak(linear_path, chromosome))
  File "/share/home/software/graph_peak_caller/graph_peak_caller/peakcollection.py", line 73, in to_approx_linear_peak
    first_node = intersecting_nodes[0]
IndexError: list index out of range

Any suggestions?

Yumin