zheminzhou/KleTy

pyarrow.lib.ArrowInvalid: Could not open Parquet input source

Opened this issue · 0 comments

Dear professor Zhou and others:
hi, We are so happy to use your new software Klety. however, the error occurred again and we can't deal with it. Can you help us ? thank you very much.
YongZhang

(KleTy) zhuy@srv1:/ahfs/ZhuY/Biosoft/biosoft/KleTy-main$ python KleTy.py -q examples/CP015990.fna
Running plasmid...Done.
Running AMR/VF gene searching...Done.
Running cgMLST...Traceback (most recent call last):
File "/ahfs/ZhuY/Biosoft/biosoft/KleTy-main/KleTy.py", line 137, in
klebtyper()
File "/home/zhuy/miniconda3/envs/KleTy/lib/python3.11/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/zhuy/miniconda3/envs/KleTy/lib/python3.11/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/zhuy/miniconda3/envs/KleTy/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/zhuy/miniconda3/envs/KleTy/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/ahfs/ZhuY/Biosoft/biosoft/KleTy-main/KleTy.py", line 110, in klebtyper
alleles, hiercc = cgmlst(tmpfile, n_thread=n_proc)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/ahfs/ZhuY/Biosoft/biosoft/KleTy-main/cgMLST.py", line 50, in cgmlst
repr_profile = pd.read_parquet(repr)
^^^^^^^^^^^^^^^^^^^^^
File "/home/zhuy/miniconda3/envs/KleTy/lib/python3.11/site-packages/pandas/io/parquet.py", line 667, in read_parquet
return impl.read(
^^^^^^^^^^
File "/home/zhuy/miniconda3/envs/KleTy/lib/python3.11/site-packages/pandas/io/parquet.py", line 274, in read
pa_table = self.api.parquet.read_table(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/zhuy/miniconda3/envs/KleTy/lib/python3.11/site-packages/pyarrow/parquet/core.py", line 1762, in read_table
dataset = ParquetDataset(
^^^^^^^^^^^^^^^
File "/home/zhuy/miniconda3/envs/KleTy/lib/python3.11/site-packages/pyarrow/parquet/core.py", line 1329, in init
[fragment], schema=schema or fragment.physical_schema,
^^^^^^^^^^^^^^^^^^^^^^^^
File "pyarrow/_dataset.pyx", line 1431, in pyarrow._dataset.Fragment.physical_schema.get
File "pyarrow/error.pxi", line 154, in pyarrow.lib.pyarrow_internal_check_status
File "pyarrow/error.pxi", line 91, in pyarrow.lib.check_status
pyarrow.lib.ArrowInvalid: Could not open Parquet input source '': Parquet magic bytes not found in footer. Either the file is corrupted or this is not a parquet file.