Using kde ErrorModel problem!

[Wanli-HE]

hi, when i used the tested data set, the error was raised, like this! do you know was happended?

iss generate --genomes SRS121011.fasta --model miseq --output miseq_reads

INFO:iss.app:Starting iss generate INFO:iss.app:Using kde ErrorModel Traceback (most recent call last): File "/mibi/Wanli/anaconda/envs/wanli/bin/iss", line 10, in sys.exit(main()) File "/mibi/Wanli/anaconda/envs/wanli/lib/python3.6/site-packages/iss/app.py", line 489, in main args.func(args) File "/mibi/Wanli/anaconda/envs/wanli/lib/python3.6/site-packages/iss/app.py", line 61, in generate_reads err_mod = kde.KDErrorModel(npz) File "/mibi/Wanli/anaconda/envs/wanli/lib/python3.6/site-packages/iss/error_models/kde.py", line 43, in init self.quality_forward = self.error_profile['quality_hist_forward'] File "/mibi/Wanli/anaconda/envs/wanli/lib/python3.6/site-packages/numpy/lib/npyio.py", line 262, in getitem pickle_kwargs=self.pickle_kwargs) File "/mibi/Wanli/anaconda/envs/wanli/lib/python3.6/site-packages/numpy/lib/format.py", line 722, in read_array raise ValueError("Object arrays cannot be loaded when " ValueError: Object arrays cannot be loaded when allow_pickle=False

[HadrienG]

Hi!

Could you tell me which version of both InSilicoseq and numpy you are using?

you can check numpy's version number interactively with:

import numpy
print(numpy.__version__)

[maojanlin]

Hi, I also encounter this issue with numpy (1.22.3) and InSilicoSeq(1.3.5). It seems that numpy change NpzFile class parameter allow_pickle default to False. (in the numpy/lib/npyio.py) I can resolve this issue by manually changing numpy/lib/npyio.py from my conda environment, but it would be nice if InSilicoSeq can resolve this in the first place. Thank you!