Error Processing Delly Structural Variants VCF file ("No objects to concatenate")

[lakshsesh97]

Hi!
I am getting an error processing structural variant form a vcf file geenrated with Delly while trying to generate the matrix. The error is below:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/miniconda3/envs/sig_test/lib/python3.11/site-packages/SigProfilerMatrixGenerator/scripts/SVMatrixGenerator.py", line 1020, in generateSVMatrix
    matrix = tsv2matrix(all_samples, project, output_dir)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/miniconda3/envs/sig_test/lib/python3.11/site-packages/SigProfilerMatrixGenerator/scripts/SVMatrixGenerator.py", line 1238, in tsv2matrix
    df = pd.concat(sv_bedpe_list)  # one master table with all samples
         ^^^^^^^^^^^^^^^^^^^^^^^^
  File "miniconda3/envs/sig_test/lib/python3.11/site-packages/pandas/core/reshape/concat.py", line 382, in concat
    op = _Concatenator(
         ^^^^^^^^^^^^^^
  File "miniconda3/envs/sig_test/lib/python3.11/site-packages/pandas/core/reshape/concat.py", line 445, in __init__
    objs, keys = self._clean_keys_and_objs(objs, keys)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "miniconda3/envs/sig_test/lib/python3.11/site-packages/pandas/core/reshape/concat.py", line 507, in _clean_keys_and_objs
    raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate

Is there a solution to this?
Any help would be much appreciated!
Thank you!

[antoniakowalewski]

I was getting the exact same error. You need to include a "sample" column after the "end2" column in your bedpe input files. See the example bedpes here: SigProfilerMatrixGenerator/references/SV/example_input/560-Breast

[lakshsesh97]

Ahh I see @antoniakowalewski Thanks! I'll try this :)