wdecoster
commented
1 year ago The error comes from gzip and biopython, both used to parse your fastq file. It seems your fastq file has a .gz extension, but could it be that it is actually not compressed? What do you get with the file command on your input file, e.g. file reads.fastq.gz?
Hi there.
I'm trying to run NanoPlot on a dataset but I'm getting this error:
concurrent.futures.process._RemoteTraceback: """ Traceback (most recent call last): File "/apps/chpc/bio/anaconda3-2020.02/envs/NanoPlot/lib/python3.7/concurrent/futures/process.py", line 239, in _process_worker r = call_item.fn(*call_item.args, *call_item.kwargs) File "/apps/chpc/bio/anaconda3-2020.02/envs/NanoPlot/lib/python3.7/concurrent/futures/process.py", line 198, in _process_chunk return [fn(args) for args in chunk] File "/apps/chpc/bio/anaconda3-2020.02/envs/NanoPlot/lib/python3.7/concurrent/futures/process.py", line 198, in
return [fn(*args) for args in chunk]
File "/apps/chpc/bio/anaconda3-2020.02/envs/NanoPlot/lib/python3.7/site-packages/nanoget/extraction_functions.py", line 388, in process_fastq_rich
for record in SeqIO.parse(inputfastq, "fastq"):
File "/apps/chpc/bio/anaconda3-2020.02/envs/NanoPlot/lib/python3.7/site-packages/Bio/SeqIO/Interfaces.py", line 74, in next
return next(self.records)
File "/apps/chpc/bio/anaconda3-2020.02/envs/NanoPlot/lib/python3.7/site-packages/Bio/SeqIO/QualityIO.py", line 1085, in iterate
for title_line, seq_string, quality_string in FastqGeneralIterator(handle):
File "/apps/chpc/bio/anaconda3-2020.02/envs/NanoPlot/lib/python3.7/site-packages/Bio/SeqIO/QualityIO.py", line 961, in FastqGeneralIterator
for line in handle:
File "/apps/chpc/bio/anaconda3-2020.02/envs/NanoPlot/lib/python3.7/gzip.py", line 300, in read1
return self._buffer.read1(size)
File "/apps/chpc/bio/anaconda3-2020.02/envs/NanoPlot/lib/python3.7/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/apps/chpc/bio/anaconda3-2020.02/envs/NanoPlot/lib/python3.7/gzip.py", line 474, in read
if not self._read_gzip_header():
File "/apps/chpc/bio/anaconda3-2020.02/envs/NanoPlot/lib/python3.7/gzip.py", line 422, in _read_gzip_header
raise OSError('Not a gzipped file (%r)' % magic)
OSError: Not a gzipped file (b'@7')
Any help will be appreciated.