Chromosome based error

[cutleraging]

Hello,

I am running your tool using:

sigSim.SigProfilerSimulator(name, \
  vcf_dir, \
  "GRCh37", \
  contexts=["96", "ID"], \
  exome=None, \
  simulations=1000, \
  updating=False, \
  bed_file=bed, \
  overlap=False, \
  gender='female', \
  chrom_based=True, \
  seed_file=None, \
  noisePoisson=False, \
  cushion=100, \
  region=None, \
  vcf=True)

But I am getting the following error:

multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/gs/gsfs0/users/rcutler/.conda/envs/SigProfilerSimulator/lib/python3.12/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
                    ^^^^^^^^^^^^^^^^^^^
  File "/gs/gsfs0/users/rcutler/.conda/envs/SigProfilerSimulator/lib/python3.12/site-packages/SigProfilerSimulator/mutational_simulator.py", line 973, in simulator
    random_sample = random.sample(list(mutation_tracker[context]),1)[0]
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gs/gsfs0/users/rcutler/.conda/envs/SigProfilerSimulator/lib/python3.12/random.py", line 430, in sample
    raise ValueError("Sample larger than population or is negative")
ValueError: Sample larger than population or is negative
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/gs/gsfs0/shared-lab/vijg-lab/2023-Ronnie/231009_multiple_ENU_analysis/SigProfilerSimulator/merged/runSigProfilerSimulator.py", line 10, in <module>
    sigSim.SigProfilerSimulator(name, \
  File "/gs/gsfs0/users/rcutler/.conda/envs/SigProfilerSimulator/lib/python3.12/site-packages/SigProfilerSimulator/SigProfilerSimulator.py", line 479, in SigProfilerSimulator
    r.get()
  File "/gs/gsfs0/users/rcutler/.conda/envs/SigProfilerSimulator/lib/python3.12/multiprocessing/pool.py", line 774, in get
    raise self._value
ValueError: Sample larger than population or is negative

When I run your tool with chrom_based=False I am able to get results. So this makes me think it is an error when wanting to have mutations simulated by chromosome. Since some of my samples don't have many mutations, I think this may be due to some chromosomes having 0 mutations. Any help with this?

Thanks, Ronnie

[mdbarnesUCSD]

Hi Ronnie,

Could you please send over an input file to reproduce this issue?

Thanks!