ValueError: Object arrays cannot be loaded when allow_pickle=False

[Coaxecva]

Hi Vitor,

I tried to run with the sample data, and had this error:

DUDes.py -s sampledata/hiseq_accuracy_k60.sam -d sampledata/arc-bac_refseq-cg_201503.npz -o sampledata/dudes_profile_output

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|		DUDes v0.08		|
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Output prefix = sampledata/dudes_profile_output
SAM (format) = sampledata/hiseq_accuracy_k60.sam (nm)
Database = sampledata/arc-bac_refseq-cg_201503.npz
Threads = 1
TaxID Start/Last rank = 1/species
Max. Read Matches = 0.000000
Min. Ref. Matches = 0.001000
Bin size = 0.250000
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Loading database file ...Traceback (most recent call last):
  File "DUDes.py", line 645, in <module>
    main()
  File "DUDes.py", line 119, in main
    refids_lookup = npzfile["refids_lookup"].item()
  File "/<path-to-python>/lib/python3.7/site-packages/numpy/lib/npyio.py", line 262, in __getitem__
    pickle_kwargs=self.pickle_kwargs)
  File "/<path-to-python>/lib/python3.7/site-packages/numpy/lib/format.py", line 692, in read_array
    raise ValueError("Object arrays cannot be loaded when "
ValueError: Object arrays cannot be loaded when allow_pickle=False

The numpy version I am using: python '3.7.3' numpy '1.16.3'.

Thanks,
Coax,

[Coaxecva]

Think you should add this option allow_pickle=True for np.load in DUDes.py:

npzfile = np.load(args.database_file, allow_pickle=True)

[pirovc]

Indeed, for any python > 3.5 the bug occurs. Thanks for the solution, I will provide a fix in the current version.

[shenwei356]

I met the same issue, and python 3.7 + numpy 1.21 still failed. Luckily it works after downgradeing numpy to 1.16.