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OSError: CRC check failed 0x4088b1f != 0xaaf28074

See original GitHub issue

Cutadapt Version: 3.3 Python Version: 3.7.7

I just installed the latest version of cutadapt, and I’m getting weird error message. I’ve previously had no issues processing this file with cutadapt.

Cutadapt is installed in my home directory on a slurm based HPC cluster. I’ve tested this on both the login node and on an interactive slurm node and I get the same error. I was hoping someone might be suggest where I can start troubleshooting.

Call to cutadapt: (base) [abf@biomix test]$ cutadapt ../fastq/WT_0_hr_1_S1_L002_R1_001.fastq.gz > test.txt

Last Passing Read (Read # 19500):

@A00547:18:HGCLFDMXX:2:1101:24795:11397 1:N:0:ATTACTCG+TATAGCCT
CGCACGCGTTAGACTCCTTGGTCCGTGTTACAAGACGGGTCGGGTGGGAAGCCGACATCGCCGCCGACCCCGTGCGCTCGGCTTCGTCGGAGACGCGTGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

First Failed Read:

@A00547:18:HGCLFDMXX:2:1101:25807:11397 1:N:0:ATTACTCG+TATAGCCT
CGCCCTAGGACACCTGCGTTACCGTTTGACAGGTGTACCGCCCCAGTCAAACTCCCCACCTGGCACTGTCCCCGGAGCGGGTCGCGCCCGCCCGCACGCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Error Message:
This is cutadapt 3.3 with Python 3.7.7
Command line parameters: ../fastq/WT_0_hr_1_S1_L002_R1_001.fastq.gz
Processing reads on 1 core in single-end mode ...
Traceback (most recent call last):
  File "/home/abf/.local/bin/cutadapt", line 8, in <module>
    sys.exit(main_cli())
  File "/home/abf/.local/lib/python3.7/site-packages/cutadapt/__main__.py", line 848, in main_cli
    main(sys.argv[1:])
  File "/home/abf/.local/lib/python3.7/site-packages/cutadapt/__main__.py", line 913, in main
    stats = r.run()
  File "/home/abf/.local/lib/python3.7/site-packages/cutadapt/pipeline.py", line 866, in run
    (n, total1_bp, total2_bp) = self._pipeline.process_reads(progress=self._progress)
  File "/home/abf/.local/lib/python3.7/site-packages/cutadapt/pipeline.py", line 326, in process_reads
    for read in self._reader:
  File "src/dnaio/_core.pyx", line 173, in fastq_iter
  File "/home/abf/anaconda3/lib/python3.7/gzip.py", line 287, in read
    return self._buffer.read(size)
  File "/home/abf/anaconda3/lib/python3.7/_compression.py", line 68, in readinto
    data = self.read(len(byte_view))
  File "/home/abf/anaconda3/lib/python3.7/gzip.py", line 465, in read
    self._read_eof()
  File "/home/abf/anaconda3/lib/python3.7/gzip.py", line 512, in _read_eof
    hex(self._crc)))
OSError: CRC check failed 0x4088b1f != 0xaaf28074