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WGLab / LinkedSV

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IndexError: index -1 is out of bounds for axis 0 with size 0 / Can I use reference genomes from other species (e.g. wildlife)？ #34

Closed kuangzhuoran closed 2 months ago

kuangzhuoran commented 2 months ago

Can I use reference genomes from other species (e.g. wildlife) My command is : "pythonlinkedsv.py -i Klg2.chr11.bam -d Klg2 -r chr11.fa -t 4 --somatic_mode" I didn't set the -v parameter

Here are my logs: [09/11/2024 19:08:05 (146.670 MB)] searching for extremely high coverage region [09/11/2024 19:08:09 (145.699 MB)] calculating distribution parameters [09/11/2024 19:08:09 (145.699 MB)] total number of reads in the genome is: 1948265 [09/11/2024 19:08:09 (145.699 MB)] calculating fragment parameters from file: /beegfs/home/kuangzhuoran/workspace/Migration/08.Inversion/02.link.read/04.LinkedSV/Klg9/Klg9.chr11.bam.bcd22 [09/11/2024 19:08:09 (145.699 MB)] N95_fragment_length is: -1 Traceback (most recent call last): File "/beegfs/home/kuangzhuoran/software/LinkedSV/linkedsv.py", line 313, in main() File "/beegfs/home/kuangzhuoran/software/LinkedSV/linkedsv.py", line 47, in main detect_increased_fragment_ends(args, dbo_args, endpoint_args) File "/beegfs/home/kuangzhuoran/software/LinkedSV/linkedsv.py", line 208, in detect_increased_fragment_ends global_distribution.estimate_global_distribution(args, dbo_args, endpoint_args, endpoint_args.bcd22_file) File "/beegfs/home/kuangzhuoran/software/LinkedSV/scripts/global_distribution.py", line 133, in estimate_global_distribution get_fragment_parameters(args, dbo_args, endpoint_args, global_dist_fp, target_bcd22_file, is_fast_mode) File "/beegfs/home/kuangzhuoran/software/LinkedSV/scripts/global_distribution.py", line 213, in get_fragment_parameters args.fragment_length_lmda = fit_geometric_distribution(frm_length_list, readpair = False) File "/beegfs/home/kuangzhuoran/software/LinkedSV/scripts/global_distribution.py", line 171, in fit_geometric_distribution k = np.percentile(length_list, cdf2) File "/beegfs/home/kuangzhuoran/miniconda3/envs/zhuoran/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4283, in percentile return _quantile_unchecked( File "/beegfs/home/kuangzhuoran/miniconda3/envs/zhuoran/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4555, in _quantile_unchecked return _ureduce(a, File "/beegfs/home/kuangzhuoran/miniconda3/envs/zhuoran/lib/python3.10/site-packages/numpy/lib/function_base.py", line 3823, in _ureduce r = func(a, **kwargs) File "/beegfs/home/kuangzhuoran/miniconda3/envs/zhuoran/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4722, in _quantile_ureduce_func result = _quantile(arr, File "/beegfs/home/kuangzhuoran/miniconda3/envs/zhuoran/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4831, in _quantile slices_having_nans = np.isnan(arr[-1, ...]) IndexError: index -1 is out of bounds for axis 0 with size 0

kuangzhuoran commented 2 months ago

Sorry, Maybe I do not provide “black_region_bed” and "gap_region_bed". I am rerunning the program

kuangzhuoran commented 2 months ago

Well, Providing “black_region_bed” and "gap_region_bed" did not make sense

kuangzhuoran commented 2 months ago

The paths for pigz and unpigz are incorrect. Creating symbolic links should resolve the issue.

Like: ln -s ~/software/LinkedSV/pigz/unpigz ~/software/LinkedSV/bin ln -s ~/software/LinkedSV/pigz/pigz ~/software/LinkedSV/bin