Braker - gc_content.stderr

Question

[Mia]

Good day! I am new to genome annotation. I want to annotate my genome using the Braker tool. I assembled my sample using SOAPdenovo2 and got a genome size of 1.3Gb, now when I try to annotate my genome I get a GC content error (I have shared the error below). The input files I used were my genome and protein files.

Command:

BRAKER/scripts/braker.pl --genome=./LM.scafSeq.masked --prot_seq=/home/data/Plant_nt.fna --AUGUSTUS_CONFIG_PATH=/home/tools/Augustus/config/ --AUGUSTUS_BIN_PATH=/home/tools/Augustus/bin/ --AUGUSTUS_SCRIPTS_PATH=/home/tools/Augustus/scripts/ --GENEMARK_PATH=/home/Tools/gmes_linux_64_4/ --PROTHINT_PATH=/home/tools/ProtHint/bin/ --TSEBRA_PATH=/home/tools/TSEBRA/bin/ --threads=18 --gff3

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Fri Sep : Log information is stored in file /home/data/braker/braker.log
ERROR in file /home/tools/BRAKER/scripts/braker.pl at line 5826
failed to execute: /home/tools/BRAKER/scripts/get_gc_content.py --sequences /home/data/LM.scafSeq.masked --print_sequence_length 1> /home/data/braker/gc_content.out 2> /home/data/braker/errors/gc_content.stderr!

braker.log

   Fri Sep : getting GC content of the genome
    /home/tools/BRAKER/scripts/get_gc_content.py --sequences /home/data/LM.scafSeq.masked --print_sequence_length 1> /home/data/braker/gc_content.out 2> /home/data/braker/errors/gc_content.stderr

gc_content.stderr

Traceback (most recent call last):
File "/home/tools/BRAKER/scripts/get_gc_content.py", line 217, in
main()
File "/home/tools/BRAKER/scripts/get_gc_content.py", line 88, in main
print_gc_range(gc_content)
File "/home/tools/BRAKER/scripts/get_gc_content.py", line 138, in print_gc_range
gc_range.append(get_percentile(all_slices, p))
File "/home/tools/BRAKER/scripts/get_gc_content.py", line 143, in get_percentile
return np.percentile(array, q)
File "<array_function internals>", line 180, in percentile
File "/home/miniconda3/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4166, in percentile
return _quantile_unchecked(
File "/home/miniconda3/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4424, in _quantile_unchecked
r, k = _ureduce(a,
File "/home/miniconda3/lib/python3.10/site-packages/numpy/lib/function_base.py", line 3725, in _ureduce
r = func(a, **kwargs)
File "/home/miniconda3/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4593, in _quantile_ureduce_func
result = _quantile(arr,
File "/home/miniconda3/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4699, in _quantile
take(arr, indices=-1, axis=DATA_AXIS)
File "<array_function internals>", line 180, in take
File "/home/miniconda3/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 190, in take
return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
File "/home/miniconda3/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 57, in _wrapfunc
return bound(*args, **kwds)
IndexError: cannot do a non-empty take from an empty axes.