ValueError: maximum supported dimension for an ndarray is 32, found 400000 #246
Description
Hi. I'm trying to generate reads with this command but I'm getting an error:
Here are a few lines from the error log:
Process Process-4:
Traceback (most recent call last):
File "/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.7.9/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.7.9/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/home/nina7/projects/ctb-noncodo/nina7/NanoSim/src/simulator.py", line 834, in simulation_aligned_metagenome
np.random.lognormal(np.log(median_l), sd_l, remaining_segments)
File "mtrand.pyx", line 3015, in numpy.random.mtrand.RandomState.lognormal
File "_common.pyx", line 598, in numpy.random._common.cont
ValueError: maximum supported dimension for an ndarray is 32, found 400000
Here's the command I used:
$nanosim/src/simulator.py metagenome -gl $nanosim/genome_list.tsv \ -a $nanosim/abundance.tsv -dl $nanosim/dna_type_list.tsv \ -c $nanosim/training_Merlin/nanosim_training_Merlin --perfect \ -med 700 -sd 2.845 -o $outdir/${i}_def_readlen -t 4
I tried running the same command without -med 700 -sd 2.845 and it worked fine. But I would also like to generate reads similar to the profile of my actual sequencing results so I wanted to use the parameters.
Would appreciate your help. Thank you!
Nina