Some entries in x0 lay outside the specified bounds

[laijirong]

Hi,
Thank you so much for developing such an amazing tool, but I met some problems while processing my datasets:

1. ntcard process: ntcard only uses 2 threads due to 2 files take in though I specified 32.

ntcard -k 19 -t 32 -p Ap /dev/shm/Ap_R1.fq.gz /dev/shm/Ap_R2.fq.gz

2. ntstat hist: I encountered the problem which confusing me much:
   cmdline:

FILE=Ap_k19.hist;ntstat hist $FILE -f plain -o ${FILE}.pdf --fit-gif ${FILE}.gif > ${FILE}.log

and the log:

Traceback (most recent call last):
  File "/share/home/laikerui/miniconda3/envs/ntstat/bin/ntstat", line 34, in <module>
    main()
    ~~~~^^
  File "/share/home/laikerui/miniconda3/envs/ntstat/bin/ntstat", line 30, in main
    exit(module.run(sys.argv[1:]))
         ~~~~~~~~~~^^^^^^^^^^^^^^
  File "/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/ntstat/hist/main.py", line 84, in run
    num_iters, final_error, history = model.fit(hist, args.ploidy, args.config)
                                      ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/ntstat/hist/model.py", line 115, in fit
    opt = scipy.optimize.differential_evolution(
        func=loss,
    ...<13 lines>...
        polish=True,
    )
  File "/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/scipy/_lib/_util.py", line 306, in wrapper
    return fun(*args, **kwargs)
  File "/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/scipy/optimize/_differentialevolution.py", line 518, in differential_evolution
    with DifferentialEvolutionSolver(func, bounds, args=args,
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^
                                     strategy=strategy,
                                     ^^^^^^^^^^^^^^^^^^
    ...<11 lines>...
                                     integrality=integrality,
                                     ^^^^^^^^^^^^^^^^^^^^^^^^
                                     vectorized=vectorized) as solver:
                                     ^^^^^^^^^^^^^^^^^^^^^^
  File "/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/scipy/optimize/_differentialevolution.py", line 997, in __init__
    raise ValueError(
        "Some entries in x0 lay outside the specified bounds"
    )
ValueError: Some entries in x0 lay outside the specified bounds

One of my data reported:

FILE=AA-india_k21.hist;ntstat hist $FILE -f plain -o ${FILE}.pdf --fit-gif ${FILE}.gif -r 1:150 > ${FILE}.log
/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/ntstat/hist/model.py:10: RuntimeWarning: divide by zero encountered in scalar divide
  rvs = [scipy.stats.gamma(params[1], params[2], 1 / params[3])]
/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/ntstat/hist/model.py:10: RuntimeWarning: divide by zero encountered in scalar divide
  rvs = [scipy.stats.gamma(params[1], params[2], 1 / params[3])]
/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/ntstat/hist/model.py:10: RuntimeWarning: divide by zero encountered in scalar divide
  rvs = [scipy.stats.gamma(params[1], params[2], 1 / params[3])]
/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/scipy/stats/_distn_infrastructure.py:2088: RuntimeWarning: invalid value encountered in divide
  place(output, cond, self._pdf(*goodargs) / scale)
/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/ntstat/hist/model.py:10: RuntimeWarning: divide by zero encountered in scalar divide
  rvs = [scipy.stats.gamma(params[1], params[2], 1 / params[3])]
/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/ntstat/hist/model.py:10: RuntimeWarning: divide by zero encountered in scalar divide
  rvs = [scipy.stats.gamma(params[1], params[2], 1 / params[3])]
/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/ntstat/hist/model.py:10: RuntimeWarning: divide by zero encountered in scalar divide
  rvs = [scipy.stats.gamma(params[1], params[2], 1 / params[3])]
/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/ntstat/hist/model.py:10: RuntimeWarning: divide by zero encountered in scalar divide
  rvs = [scipy.stats.gamma(params[1], params[2], 1 / params[3])]
/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/ntstat/hist/model.py:10: RuntimeWarning: divide by zero encountered in scalar divide
  rvs = [scipy.stats.gamma(params[1], params[2], 1 / params[3])]
/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/ntstat/hist/model.py:10: RuntimeWarning: divide by zero encountered in scalar divide
  rvs = [scipy.stats.gamma(params[1], params[2], 1 / params[3])]
/share/home/laikerui/miniconda3/envs/ntstat/lib/python3.13/site-packages/ntstat/hist/model.py:10: RuntimeWarning: divide by zero encountered in scalar divide
  rvs = [scipy.stats.gamma(params[1], params[2], 1 / params[3])]

Can you give me some advice?

Best regards,
Lai.

AA-india_k21.hist.txt
Ap_k19.hist.txt