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tombo preprocess annotate_raw_with_fastqs have error?
tombo preprocess annotate_raw_with_fastqs --fast5-basedir rawdata/ --fastq-filenames output/b2-merge/meth.fq.gz --overwrite [15:54:00] Preparing reads and extracting read identifiers. ****** WARNING ****** Basecalls exsit in specified slot for some reads. Set --overwrite option to overwrite these basecalls. 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 28/28 [00:00<00:00, 276.40it/s] [15:54:00] Annotating FAST5s with sequence from FASTQs. Process Process-4: Traceback (most recent call last): File "/home/xugang/anaconda3/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/xugang/anaconda3/lib/python3.8/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/app/tombo/tombo/_preprocess.py", line 148, in _feed_seq_records_worker fastq_rec = list(islice(fastq_fp, 4)) File "/home/xugang/anaconda3/lib/python3.8/codecs.py", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
This command does not accept gzipped input sequences. If you unzip the fastq file and retry the command it should work.