Closed imdanique closed 8 months ago
Do your VCF files contain alternative chromosomes? The program does not support VCF files that include alternative chromosomes.
@farhangus I don't have alternative contigs and I've removed all the variants from unlocalized and unplaced (random) sequences but still get the same error
will you please send me your vcf file ("fjaryanius@gmail.com"), so I can check it
Have the above errors been resolved? I also encountered the same problem
will you please send me your vcf file ("fjaryanius@gmail.com"), so I can check it
The problem is solved in the latest version of the program.
Hi, sorry for bothering again but it still gives me an error. Almost the same as previous one:
$python -m sniffles2_plot -i merged -o .
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/__main__.py", line 9, in <module>
entry_point()
File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/cli/entry_point.py", line 39, in entry_point
generate_charts(file_name, directory_path)
File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/cli/generate_charts.py", line 23, in generate_charts
generate_multi_vcf_charts(input_vcf_file_path, output_directory_path)
File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/cli/multi_vcf_visualizer.py", line 23, in generate_multi_vcf_charts
SV_site.sv_sites_per_genome()
File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/chart_generator/sv_sites_per_genome.py", line 38, in sv_sites_per_genome
obj = VCFLineSVPopulation(line)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/parser/vcf_line_parser.py", line 272, in __init__
self.get_genotype(FORMAT, sample_header_names)
File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/parser/vcf_line_parser.py", line 344, in get_genotype
sample_gt.set_dv(gt_value)
File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/parser/vcf_line_parser.py", line 198, in set_dv
self.dv = int(this_dv)
^^^^^^^^^^^^
ValueError: invalid literal for int() with base 10: '.\n'
Thanks for your message, will you please send me your VCF file, so I can check the program.
On Thu, Feb 1, 2024 at 7:18 AM Daniyar Karabayev @.***> wrote:
Hi, sorry for bothering again but it still gives me an error. Almost the same as previous one:
$python -m sniffles2_plot -i merged -o .
Traceback (most recent call last): File "
", line 198, in _run_module_as_main File " ", line 88, in _run_code File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/main.py", line 9, in entry_point() File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/cli/entry_point.py", line 39, in entry_point generate_charts(file_name, directory_path) File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/cli/generate_charts.py", line 23, in generate_charts generate_multi_vcf_charts(input_vcf_file_path, output_directory_path) File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/cli/multi_vcf_visualizer.py", line 23, in generate_multi_vcf_charts SV_site.sv_sites_per_genome() File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/chart_generator/sv_sites_per_genome.py", line 38, in sv_sites_per_genome obj = VCFLineSVPopulation(line) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/parser/vcf_line_parser.py", line 272, in init self.get_genotype(FORMAT, sample_header_names) File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/parser/vcf_line_parser.py", line 344, in get_genotype sample_gt.set_dv(gt_value) File "/Users/karabaye/miniconda3/envs/assemblies/lib/python3.12/site-packages/sniffles2_plot/parser/vcf_line_parser.py", line 198, in set_dv self.dv = int(this_dv) ^^^^^^^^^^^^ ValueError: invalid literal for int() with base 10: '.\n' — Reply to this email directly, view it on GitHub https://github.com/farhangus/Sniffles2_plot/issues/7#issuecomment-1921305860, or unsubscribe https://github.com/notifications/unsubscribe-auth/A73J5UIUSJXVUCEJ6XRTQ2DYROIYVAVCNFSM6AAAAAA6MDKEQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRRGMYDKOBWGA . You are receiving this because you modified the open/close state.Message ID: @.***>
The tool runs correctly with single-sample vcf files, however when I try to run a vcf file with 3 samples it throws an error