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Posted on In
Symbols count in article: 7.9k Reading time ≈ 7 mins.

Problem Background

Sometimes we want to figure out whether the error rate of the nanopore sequencing is equalized with different nanopore channels.

So we need to group the sequenced data into different channels.

But due to the format of fastq file shown below, we cannot directly obtain the channel information of the specified sequence id with module Biopython(click to enter).

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Posted on Edited on In
Symbols count in article: 3.7k Reading time ≈ 3 mins.

Problems encountered on 26/09/2022

Problem Situation

When I tried to run baseLess, an error occured：

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Traceback (most recent call last):
  File "/home/zxy/anaconda3/envs/baseLess/bin/baseLess", line 11, in <module>
    sys.exit(main())
  File "/home/zxy/anaconda3/envs/baseLess/lib/python3.10/site-packages/baseLess/__main__.py", line 55, in main
    args.func(args)
  File "/home/zxy/anaconda3/envs/baseLess/lib/python3.10/site-packages/baseLess/db_building/build_db.py", line 44, in main
    tr = TrainingRead(f, normalization=args.normalization,
  File "/home/zxy/anaconda3/envs/baseLess/lib/python3.10/site-packages/baseLess/db_building/TrainingRead.py", line 74, in __init__
    self.raw = None
  File "/home/zxy/anaconda3/envs/baseLess/lib/python3.10/site-packages/baseLess/db_building/TrainingRead.py", line 163, in raw
    raw = self.hdf[f'Raw/Reads/{raw_varname}/Signal'][()]
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/home/zxy/anaconda3/envs/baseLess/lib/python3.10/site-packages/h5py/_hl/dataset.py", line 710, in __getitem__
    return self._fast_reader.read(args)
  File "h5py/_selector.pyx", line 366, in h5py._selector.Reader.read
OSError: Can't read data (can't open directory: /home/zxy/anaconda3/envs/baseLess/lib/hdf5/plugin)
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